nmaCHARMM.pl

Usage

usage:   nmaCHARMM.pl [options] [PDBfile]
options: [-modes value]
         [-xtract prefix]
         [-minimize steps]
         [-minout file]
         [-block]
         [-quasi dcdfile] [-temp value]
         [-quasel selection]
         [-ic] [-icscale value]
         [-ics angle=value,bond=value,dihedral=value modefile]
         [-dihedsample modefile prefix from to delta]
         [-entropy]
         [-psf PSFfile CRDfile]
         [-par CHARMMparams]
         [-log logFile] [-cmd logFile]
         [-custom file]

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Description

This script carries out normal-mode and quasiharmonic analysis through CHARMM. It relies primarily on the CHARMM all-atom force field, with the option to use the block normal-mode method for large systems. In principle this script could also be used for elastic network model mode analysis if an model is constructed and given as an alternative force field.

Options

-help 

usage information

-modes value 

number of modes to calculate

-xtract prefix 

extract modes to files with given prefix

-minimize steps 

minimize structure before carrying out NMA calculation

-minout file 

write out minimized structure to file

-block 

carry out block normal-mode calculation

-quasi dcdfile 

carry out quasi-harmonic analysis from trajectory file

-temp value 

temperature for quasi-harmonic analysis

-ic 

carry out normal-mode analysis in internal coordinate space

-icscale value 

overall scaling factor (1/factor) for extrapolating coordinates along internal coordinate normal modes

-ics key=value[,..] modefile 

extrapolate coordinates along internal coordinate normal modes with separate scaling factors for bonds, angles, and dihedrals

-dihedsample modefile prefix from to delta 

extrapolate coordinates along dihedral coordinate over given range (from-to, steps according to delta)

-entropy 

calculate vibrational entropy from normal modes

-psf PSFfile CRDfile 

use CHARMM PSF and CRD files to setup structure

-par key=value[,...] 

set CHARMM parameters

-log file 

output CHARMM log file

-cmd file 

output CHARMM input file

-custom file 

provide custom CHARMM input file