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]

Show source

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