MMTSB
Tool Set Documentation

mdCHARMM.pl

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Usage

usage:    mdCHARMM.pl [options] PDBfile
options:  [-restart filename]
          [-enerout file] [-trajout file]
          [-restout file] [-final pdb]
          [-crdout file]
          [-nochain]
          [-elog file] [-log file]
          [-cmd file]
          [-stdout tag]
          [-par CHARMMparams]
          [-psf PSFfile CRDfile]
          [-mol2 MOL2file]
          [-boxsizefromrestart file]
          [-l [ca|cb|cab|cabp|heavy] force refpdb|self min:max[=...]]
          [-cons [ca|cb|cab|cabp|heavy] refpdb|self min:max[_force][=...]]
          [-rmsd [ca|cb|cab|cabp|heavy] refpdb refval min:max[_force][=...]]
          [-hmcm chainFile min:max[_force][=...]]
          [-custom file]
          [-comp PDBfile]
          [-charmmexec charmmexec]
Show source


Description

This script allows running molecular dynamics simulations with CHARMM. It is intended primarily for running protein simulations with implicit solvent in the NVT ensemble. Particle Mesh Ewald electrostatics, Langevin dynamics, periodic boundaries, NPT ensembles and other more advanced simulation features are not supported at this point but may be added in the future.

Simulation parameters are set with -par. A list of available parameters is given here. Various restraints can be set with -l, -cons, and -hmcm as in minCHARMM.pl

The remaining options are used to set input and output files. With -stdout a common tag may be given to generate the standard set of output files. To set file names individual files the options -enerout, -trajout, -restout, -final, -elog, -log, -cmd are available for the trajectory output file, the restart output file, a PDB file with the final conformation, an energy log file, a CHARMM log file, and commands sent to CHARMM, respectively.
The option -restart is available to restart a simulation from a previously written restart file.

Options

-help 
usage information
-restart filename 
uses the specified CHARMM restart file
-enerout file 
generates CHARMM output file with energies
-trajout file 
generates a CHARMM trajectory file
-restout file 
generates a CHARMM restart file
-final pdb 
generates a PDB file of the last structure before exiting CHARMM
-crdout file 
writes final conformation in CRD format
-elog file 
generates an energy log file
-log file 
generates CHARMM log file
-cmd file 
generates CHARMM input file
-stdout tag 
generates standard output files
-par CHARMMparams 
specifies CHARMM parameters (see CHARMM_Parameters)
-psf PSFfile CRDfile 
uses specified protein structure file (PSF) and coordinate file (CRD)
-mol2 MOL2file 
uses specified mol2 file to setup topology
-l [ca|cb|cab|heavy] force self|refpdb [chain|segment:]min:max[_force][=...] 
a restraint is applied to all specified atoms that are not given in the residue range
-cons [ca|cb|cab|heavy] self|refpdb [chain|segment:]min:max[_force][=...] 
a harmonic restraint is applied to all specified atoms given in the residue range
-hmcm chainFile [chain|segment:]min:max[_force][=...] 
a harmonic center of mass restraint is applied to all specified atoms given in the residue range
-rmsd [ca|cb|cab|heavy] refpdb refval [chain|segment:]min:max[_force][=...] 
a rmsd-based restraint, calculated with respect to a reference structure, is applied to all specified atoms given in the residue range
-custom file[:file] 
reads in additional CHARMM commands via a custom file
-comp PDBfile 
loads a reference PDB file into the comparison coordinate set
-charmmexec charmmexec 
uses the specified CHARMM executable

Examples

mdCHARMM.pl -stdout 1vii.md -par dynsteps=1000 1vii.exp.min.pdb
runs 1000 steps of molecular dynamics simulation in vacuum starting from the given input file. Default output files are generated with the tag 1vii.md.


mdCHARMM.pl -par dynsteps=500,dyntemp=320,gb -restout restart 1vii.exp.min.pdb
runs 500 steps molecular dynamics simulation at 320K using GB implicit solvent. Only a restart file is written out.


mdCHARMM.pl -par dynsteps=500,dyntemp=320,gb -cons ca self 1:36_5.0 -restart restart -final - 1vii.exp.min.pdb
restarts a previous simulation and continues for another 500 steps at 320K. C-alpha coordinates are restrained to the initial position for all residues with a force constant of 5 kcal/mol. The final conformation is written to standard output.

ATOM      1  N   MET     1       2.565 -10.145  -2.776  1.00  0.00      PRO0
ATOM      2  HT1 MET     1       1.861 -10.969  -3.352  1.00  0.00      PRO0
ATOM      3  HT2 MET     1       2.432 -10.770  -1.924  1.00  0.00      PRO0
ATOM      4  HT3 MET     1       3.582  -9.705  -3.267  1.00  0.00      PRO0
ATOM      5  CA  MET     1       1.854  -8.970  -2.301  1.00  0.00      PRO0
ATOM      6  HA  MET     1       2.587  -8.278  -1.873  1.00  0.00      PRO0
ATOM      7  CB  MET     1       1.173  -8.309  -3.533  1.00  0.00      PRO0
ATOM      8  HB1 MET     1       0.642  -7.381  -3.134  1.00  0.00      PRO0
ATOM      9  HB2 MET     1       0.404  -8.936  -4.008  1.00  0.00      PRO0
ATOM     10  CG  MET     1       2.260  -7.770  -4.536  1.00  0.00      PRO0

...


mdCHARMM.pl -par dynsteps=500,dyntemp=320,gb -rmsd ca 1vii.exp.min.pdb 0.5 1:36_5.0 1vii.exp.min.pdb
starts a simulation with 500 steps at 320K. C-alpha coordinates for all residues are restrained using an RMSD-based restraint with respect to a reference structure with a force constant of 5 kcal/mol and and a reference value of 0.5 Angstroms.


mdCHARMM.pl -par dynsteps=500,dyntemp=320,gb -comp 1vii.exp.min.pdb -custom custom.file 1vii.exp.min.pdb
starts a simulation with 500 steps at 320K. Here, a custom file is used to issue an RMSD-based restraint and the reference structure is read in separately. This is example is analogous to using the -rmsd option.

* Custom Restraint
*

rgyr force 5 refe 0.5 rmsd comp ORIE -
select ( atom * * ca ) -


mdCHARMM.pl -par dynsteps=500,dyntemp=320,gb -cons ca self PRO0:1:5_5.0 1vii.exp.min.pdb
starts a simulation with 500 steps at 320K. C-alpha coordinates from residues 1 to 6 in the PRO0 segment are restrained to the initial position with a force constant of 5 kcal/mol. Providing segment or chain id may be necessary when numbering of residues in the PDB file is not contiunous.