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run.prm.full
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MCCE CONFIGURATION FILE (full 09/15/2004)
This file must have name "run.prm" in the working directory. The first
field of the line is the value, and last string with parenthesis is
the key. Entries marked with * should be configured with your run.
You need this configure file in your working directory.
You need to point out a pdb file to work on.
Optionally:
You may need file defined by "RENAME_RULES" to customize cofactors.
You may need file defined by "EXTRA" to customize advanced contols.
==============================================================================
Most modified entries
------------------------------------------------------------------------------
Input and Output:
# Input pdb file name and path
prot.pdb (INPDB)
# The steps mcce will do. 't' is true (do), 'f' is false (not do). As step 3
# and step 4 are quite time consuming, one often stops right after step 2 to
# check the status such as the number of conformers. If the number of final
# conformers exceeds 5000, then step 3 and 4 will take over a week.
Steps:
f step 1: pre-run, pdb-> mcce pdb (DO_PREMCCE)
f step 2: make rotatmers (DO_ROTAMERS)
f step 3: do energy calculations (DO_ENERGY)
f step 4: monte carlo sampling (DO_MONTE)
==============================================================================
0 sidechain optimization: 0=mcce, 1=P.Comte's GA, (SIDECHAIN_OPT)
2=mcce + MHD's pruning function
apbs Poisson-Boltzmann solver,apbs or delphi (PBE_SOLVER)
surface self/surface, APBS always use rxn self energy (RXN_METHOD)
==============================================================================
Less modified entries (Monte Carlo titration simulation)
------------------------------------------------------------------------------
# Dielectric constant of protein. Usually epsilon 8 is used for small soluble
# protein (~100 residues), and 4 is used for big trans-membrane protein
# (> 200 residues)
4.0 Protein dielectric constant for DelPhi (EPSILON_PROT)
# This file contains entries that overwrite those in the parameter directory
# and extral controls over the program.
/home/mcce/mcce2.5.1/extra.tpl (EXTRA)
# The renaming rule. It is sometimes necessary to divide a big group into
# separate ionizable groups, or put ligands and cofactor as one group. This
# can be done by renaming the atom and residue.
/home/mcce/mcce2.5.1/name.txt MCCE renaming rule. (RENAME_RULES)
# The type of simulation, pH or Eh.
ph "ph" for pH titration, "eh" for eh titration (TITR_TYPE)
# The starting pH, or the pH of Eh titration
0.0 Initial pH (TITR_PH0)
# The interval of pH titration
1.0 pH interval (TITR_PHD)
# The starting Eh, or the Eh of pH titration
0.0 Initial Eh (TITR_EH0)
# The interval of Eh titration
30.0 Eh interval (in mV) (TITR_EHD)
# Number of titration points.
15 Number of titration points (TITR_STEPS)
=============================================================================
#############################################################################
MODIFYING FOLLOWING ENTRIES REQUIRE ADVANCED KNOWLEDGE:
-----------------------------------------------------------------------------
/home/mcce/mcce2.5.1 (MCCE_HOME)
# mcce home directory, the combination of this path and diectric constant
# points to the parameter directory
t Minimize output files (MINIMIZE_SIZE)
# When this flag is "t", the program will not write these files:
# step2_out.full by step 2
# demetri_out.pdb by step 2
# hvrot.pdb by step 2
# step3_out.pdb by step 3
# mc_out by step 4
t Print trace file (DO_TRACE)
# creates a record with MCCE revision number, time and date of run, and
# all user options set in run.prm and appends it to (or creates) the
# run.trace file
Options specific to each step:
step 1:
# If this flag is on ('t'), mcce program will identify the C terminus and N
# terminus of the polypeteides based on the geometry. Terminal residues have
# extra ionizable sites than residues having peptide bonds. One needs to be
# careful if there are missing piece of peptide in the given structure.
t Label terminal residues? (TERMINALS)
#
0.1 cut off water if % SAS exceeds this number (H2O_SASCUTOFF)
2.0 distance limit of reporting clashes (CLASH_DISTANCE)
t ignore hydrogens in input structure (IGNORE_INPUT_H)
#turning off may cause error in rotatmer making
step 2:
f Use control file "head1.lst" for rotamer making (ROT_SPECIF)
t Rebuild sidechain based on torsion minima (REBUILD_SC)
t Do swap (stereo isotope) (ROT_SWAP)
t Do rotate? (PACK)
6 number of rotamers in a bond rotation (ROTATIONS)
f Do swing? (SWING)
10.0 phi in degrees of swing (PHI_SWING)
1.00 SAS cuttoff of making fewer rotamers (SAS_CUTOFF)
10.0 Cutoff of self vdw in kcal/mol (VDW_CUTOFF)
5000 number of repacks (REPACKS)
0.03 occupancy cutoff of repacks (REPACK_CUTOFF)
t h-bond directed rotamer making (HDIRECTED)
1.0 threshold for two conformers being different (HDIRDIFF)
36 Limit number of the H bond conformers (HDIRLIMT)
f Do relaxation on water (RELAX_WAT)
3.2 if distance between water and heavy atom is smaller than this, move water away (WATER_RELAX_THR)
# Relaxation
10 number of cycles to relax rotamer clash (HV_RELAX_NCYCLE)
10 time (in fs) for each relaxation iteration (HV_RELAX_DT)
10 number of iterations (HV_RELAX_NITER)
2. relax rotamer if vdw interaction is bigger than this (HV_RELAX_VDW_THR)
5. not relax rotamer if heavy atom vdw is bigger than this (HV_RELAX_HV_VDW_THR)
-1.0 relax if electrostatic interaction is more favorable than this, and the charged groups are close (HV_RELAX_ELEC_THR)
0.1 threshold used to define a charged atom, see hv_relax_elec_dist_thr (HV_RELAX_ELEC_CRG_THR)
3.0 only relax electrostatically favorable pairs that has charged atom distance shorter than this (HV_RELAX_ELEC_DIST_THR)
20. scaling factor for torsion during relaxation (HV_TORS_SCALE)
10000 maximun n steps of shake (HV_RELAX_N_SHAKE)
0.001 maximun allowance for bond length to deviate (HV_RELAX_SHAKE_TOL)
1.0 constraint distance (HV_RELAX_CONSTRAINT)
20. constraint force for atom stay in original position (HV_RELAX_CONSTRAINT_FRC)
f include neighbors when doing relaxation (expensive) (HV_RELAX_INCLUDE_NGH)
4.0 threshold for include as a neighbor during relaxation (HV_RELAX_NGH_THR)
20 the upper limit number of heavy atom rotamers (N_HV_CONF_LIMIT)
t Do relaxation on hydrogens (RELAX_H)
-5.0 Energy threshold for keeping the conformer (RELAX_E_THR)
200 Loop over N local microstates (RELAX_NSTATES)
6 default number of hydroxyl positions (RELAX_N_HYD)
5. do not relax hydrogen if vdw bwt two sidechain conformer bigger than this (RELAX_CLASH_THR)
1.0 phi for each step of relaxation (RELAX_PHI)
300 Maximum number of steps of relaxation (RELAX_NITER)
0.5 Torque threshold for keep relaxing (RELAX_TORQ_THR)
0.02 Last pruning threshold for conformers (PRUNE_THR)
0.5 Pruning cutoff of RMSD (PRUNE_RMSD)
1.0 Pruning cutoff of eletrostatic pairwise (PRUNE_ELE)
8.0 Pruning cutoff of vdw pairwise (PRUNE_VDW)
0 maximum number of conformer per residue ( 0=unlimited ) (NCONF_LIMIT)
step 3:
f Use SAS + Coulomb's law for ele interaction (QUICK_ENERGIES)
80.0 Solvent dielectric constant for DelPhi (EPSILON_SOLV)
65 Grids in each DelPhi (GRIDS_DELPHI)
2.0 The target grids per angstrom for DelPhi (GRIDS_PER_ANG)
1.4 Radius of the probe (RADIUS_PROBE)
2.0 Ion radius (IONRAD)
0.15 Salt (SALT)
/home/mcce/mcce2.5.1/bin/apbs APBS executable (APBS_EXE)
/home/mcce/mcce2.5.1/bin/delphi DelPhi executable (DELPHI_EXE)
f Reassign charge and radii before delphi(if not true then use value in PDB file) (REASSIGN)
f Recalculate torsions energy when write out head3.lst (RECALC_TORS)
step 4:
f Average the pairwise, "f" uses the smaller (AVERAGE_PAIRWISE)
20. Warnning Threshold of difference in pairwise (WARN_PAIRWISE)
5.0 Big pairwise threshold to make big list (BIG_PAIRWISE)
### Common parameters for both monte carlo
-1 Random seed, -1 uses time as random seed (MONTE_SEED)
298.15 Temperature (MONTE_T)
3 Number of flips (MONTE_FLIPS)
100 Annealing = n_start * confs (MONTE_NSTART)
500 Equalibration = n_eq * confs (MONTE_NEQ)
0.001 Cut-off occupancy of the reduction (MONTE_REDUCE)
### Only for Junjun's monte carlo
2 Number of independent monte carlo sampling (MONTE_RUNS)
2000 Sampling = n_iter * confs (MONTE_NITER)
20000 Trace energy each MONTE_TRACE steps, 0 no trace (MONTE_TRACE)
1000000 Maximum microstates for analytical solution (NSTATE_MAX)
f Specify mfe point, f=pKa/Em (MFE_POINT)
-1.0 MFE cutoff(Kcal), default 0.5 (MFE_CUTOFF)
### Only for Yifan's monte carlo
t Using Yifan's monte carlo (MONTE_ADV_OPT)
f Using format from old version (MONTE_OLD_INPUT)
5000 Min Sampling = n_iter * confs (MONTE_NITER_MIN)
-1 Max Sampling = n_iter * confs(-1 stop @ converge) (MONTE_NITER_MAX)
10000 Number of iterations each cycle (MONTE_NITER_CYCLE)
1000 niter * n_conf check convergence (MONTE_NITER_CHK)
-1 Number of the reduce steps(-1 stop @ converge) (MONTE_N_REDUCE)
0.01 Threshhold for convergence (MONTE_CONVERGE)
f Calculate free energy (MONTE_DO_ENERGY)
3000 Starting temperature for annealling (ANNEAL_TEMP_START)
10 Number of steps of annealling (ANNEAL_NSTEP)
500 Number of iterations/conformer in annealing step (ANNEAL_NITER_STEP)
# Advanced options:
1 delphi start conformer number, 0 based (PBE_START)
99999 delphi end conformer number, self included (PBE_END)
f skip delphi in step3 (DEBUG option) (SKIP_ELE)
/tmp delphi temporary file folder, "/tmp" uses node (PBE_FOLDER)
t clean up delphi focusing directory? (DELPHI_CLEAN)
debug.log (DEBUG_LOG)
new.tpl local parameter file for unrecognized res (NEWTPL)
1.7 defalut van der Waals radius, for SAS (DEFAULT_RADIUS)
0.5 factor to 1-4 LJ potontial (1.0 is full) (FACTOR_14LJ)
6.0 dielectric constant for Coulomb's law (EPSILON_COULOMB)
#APBS
65 number of grids (GRIDS_APBS)
mol protein-solvent surface definition: mol/smol/spl2/spl4 (SURFACE_APBS)
spl0 mapping the point charges to the grid: spl0/spl2/spl4 (CHARGES_APBS)
sdh type of PBE boundary condition: zero/sdh/mdh/focus (BOUND_COND_APBS)
##############################################################################
#IPECE
f add neutral atoms to simulate a membrane slab (IPECE_ADD_ME)
33. the thichness of the membrane to be add (IPECE_MEM_THICKNESS)
M the chain ID of the add atoms (IPECE_MEM_CHAINID)
###########PASCAL COMTE GENETIC ALGORITHM PARAMETERS FOR STEP 2################
-1 Random seed value, use -1 for random value (GA_SEED)
6000 Population size of each GA: use up to 20k (GA_POP_SIZE)
0.1 Mutation rate for each GA (GA_MUTATION_RATE)
0.0 Migration rate for each GA (GA_MIGRATION_RATE)
0.9 Crossover rate for each GA (GA_CROSSOVER_RATE)
30 Max nb. of rnd cut points for crossover (GA_RANDOM_CUT_POINTS)
10 Nb. of GA rounds without convergence check (GA_PHASE)
5 Nb. of GA rounds with convergence check (GA_SHIFT)
15.0 Distribution Center (GA_DIST_CENTER)
2.0 solutions within EPS*DIST.CENTER in bucket (GA_DIST_CENTER_EPS)
400000 Max nb. protein conformations in final bucket (GA_MAX_BUCKET_POP)
5.0 Local Residue lowest occupied energy cutoff (GA_RESIDUE_MIN_ENERGY_CUTOFF)
0.0 Occupied conformers in MIN_ENRG_CUTOFF are deleted (GA_OCCUPANCY_CUTOFF)
0.7 Pop. % for dE calculation (GA_DELTA_E)
-1 Disabled when -1 (GA_SPHERE_FOCUS_RESID)
20.0 Up to how many Angstorms to include residues (GA_SPHERE_PROBE_RADIUS)
0 GA output format: 0 display screen, 1 file (GA_OUTPUT)
###########PASCAL COMTE GENETIC ALGORITHM PARAMETERS FOR STEP 2################