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nmaCHARMM.pl
From MMTSB
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]
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
- 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