MdCHARMM.pl

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 <A HREF="http://mmtsb.scripps.edu/cgi-bin/charmmpar" TARGET=cpar>here</A>. Various restraints can be set with -l, -cons, and -hmcm as in <docmark>minCHARMM.pl</docmark>

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

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

...