Merge pull request #156 from zhang-ivy/convert-glycans

Enable GLYCAM06j-1 forcefield conversion

amber/files/glycam/Glycoprotein_shortened.leapin

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+source oldff/leaprc.ff14SB
+source leaprc.GLYCAM_06j-1
+
+## Testing residues made for linking to proteins.
+##
+## Testing RES-ALA-RES-ALA-RES to ensure that we have tried a decent
+## set of linkage environments.
+## See definitions in the script that created this file for details.
+##
+
+# set 0 -- HYP (not for linking -- prerequisite for OLP)
+ m2 = sequence { NHYP ALA HYP ALA CHYP }
+ impose m2 { 1 2 3 4 5 } { { "N" "CA" "C" "N" 90.0 } }
+
+#m2 = sequence { NALA ALA HYP ALA CHYP }
+#m2 = sequence { ROH 0GA }
+
+# set 1 -- OLT
+ m3 = sequence { NOLT ALA OLT ALA COLT }
+ set m3 tail m3.1.OG1
+ m3 = sequence { m3 0GB }
+ set m3 tail m3.3.OG1
+ m3 = sequence { m3 0GB }
+ set m3 tail m3.5.OG1
+ m3 = sequence { m3 0GB }
+ impose m3 { 1 2 3 4 5 } { { "N" "CA" "C" "N" 90.0 } }
+
+# set 2 -- OLS
+ m4 = sequence { NOLS ALA OLS ALA COLS }
+ set m4 tail m4.1.OG
+ m4 = sequence { m4 0GB }
+ set m4 tail m4.3.OG
+ m4 = sequence { m4 0GB }
+ set m4 tail m4.5.OG
+ m4 = sequence { m4 0GB }
+ impose m4 { 1 2 3 4 5 } { { "N" "CA" "C" "N" 90.0 } }
+
+# set 3 -- OLP
+ m5 = sequence { NOLP ALA OLP ALA COLP }
+ set m5 tail m5.1.OD1
+ m5 = sequence { m5 0GB }
+ set m5 tail m5.3.OD1
+ m5 = sequence { m5 0GB }
+ set m5 tail m5.5.OD1
+ m5 = sequence { m5 0GB }
+ impose m5 { 1 2 3 4 5 } { { "N" "CA" "C" "N" 90.0 } }
+
+# set 4 -- NLN
+ m6 = sequence { NNLN ALA NLN ALA CNLN }
+ set m6 tail m6.1.ND2
+ m6 = sequence { m6 0GB }
+ set m6 tail m6.3.ND2
+ m6 = sequence { m6 0GB }
+ set m6 tail m6.5.ND2
+ m6 = sequence { m6 0GB }
+ impose m6 { 1 2 3 4 5 } { { "N" "CA" "C" "N" 90.0 } }
+
+
+##
+## Built 5 molecules
+## Now, translate them away from each other
+##
+ translate m2 { 0.0 60.0 0.0 } 
+ translate m3 { 30.0 0.0 0.0 }
+ translate m4 { 30.0 30.0 0.0 }
+ translate m5 { 30.0 60.0 0.0 } 
+ translate m6 { 60.0 0.0 0.0 }
+
+Glycoprotein = combine { m2 m3 m4 m5 m6 }
+
+saveamberparm Glycoprotein Glycoprotein_shortened.parm7 Glycoprotein_shortened.rst7
+
+quit
+

amber/files/glycam/leaprc.GLYCAM_06j-1

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+# ----- leaprc for loading the Glycam_06 carbohydrate force field
+# also contains atom types for lipids
+#
+# load atom type hybridizations
+# (includes atom types relevant to lipids)
+#
+addAtomTypes {
+ { "C" "C" "sp2" }
+ { "Cg" "C" "sp3" }
+ { "Cy" "C" "sp3" }
+ { "Ck" "C" "sp2" }
+ { "CT" "C" "sp3" }
+ { "Cj" "C" "sp2" }
+ { "Cp" "C" "sp3" } 
+ { "H" "H" "sp3" }
+ { "H1" "H" "sp3" }
+ { "H2" "H" "sp3" }
+ { "Ha" "H" "sp3" }
+ { "Hp" "H" "sp3" } 
+ { "Hc" "H" "sp3" }
+ { "Ho" "H" "sp3" }
+ { "HW" "H" "sp3" }
+ { "Ng" "N" "sp2" }
+ { "NT" "N" "sp3" }
+ { "N3" "N" "sp3" } 
+ { "Oh" "O" "sp3" }
+ { "Os" "O" "sp3" }
+ { "O" "O" "sp2" }
+ { "O2" "O" "sp2" }
+ { "OW" "O" "sp3" }
+ { "Oy" "O" "sp3" }
+ { "S" "S" "sp3" }
+ { "Sm" "S" "sp3" }
+ { "P" "P" "sp3" } 
+}
+#
+# load the main paramter set
+#
+glycam_06 = loadamberparams GLYCAM_06j.dat
+##
+#
+# load all prep files for polysaccharides
+#
+#loadamberprep GLYCAM_06j-1.prep
+# Instead of loading prep file above, load lib (generated from the prep file)
+loadOff ../../glycam/GLYCAM_06j-1.lib
+#
+# load lib files
+#
+# for attaching glycans to proteins
+loadOff GLYCAM_amino_06j_12SB.lib
+loadOff GLYCAM_aminoct_06j_12SB.lib
+loadOff GLYCAM_aminont_06j_12SB.lib
+## add residue maps for linking glycans to proteins
+## Note! use of these requires sourcing the ff12SB leaprc and loading the amino 
+## libraries commented out in the load libs section 
+addPdbResMap { 
+ { 0 "OLS" "NOLS" } { 1 "OLS" "COLS" }
+ { 0 "OLT" "NOLT" } { 1 "OLT" "COLT" }
+ { 0 "OLP" "NOLP" } { 1 "OLP" "COLP" }
+ { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
+ { 0 "NLN" "NNLN" } { 1 "NLN" "CNLN" }
+} 
+#
+# for explicit solvent and ions
+#
+# the following assumes most users want to use tip3p as the 
+# explicit solvent model 
+# this can easily switched by the following commands in leap:
+# WAT = TP5
+# loadamberparams frcmod.tip5p
+#
+loadOff solvents.lib # solvents 
+HOH = TP3 # set default water model
+WAT = TP3 
+loadOff atomic_ions.lib # load ions library
+# to use ions for TIP5P, you will need to use a different frcmod below
+# If desired, see the AMBER manual for additional ion force field options.
+ionsff = loadamberparams frcmod.ionsjc_tip3p # set ion params for TIP3P