MMTSB
Tool Set Documentation

nmaCHARMM.pl

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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


Description

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 
 ?
-ics ? 
-dihedsample ?
-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

Examples