MMTSB
Tool Set Documentation

Difference between revisions of "nmaCHARMM.pl"

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Line 18: Line 18:
 
; -temp value : temperature for quasi-harmonic analysis
 
; -temp value : temperature for quasi-harmonic analysis
 
; -ic : carry out normal-mode analysis in internal coordinate space
 
; -ic : carry out normal-mode analysis in internal coordinate space
; -icscale value : ?
+
; -icscale value : overall scaling factor (1/factor) for extrapolating coordinates along internal coordinate normal modes
; -ics ? :
+
; -ics key=value[,..] modefile : extrapolate coordinates along internal coordinate normal modes with separate scaling factors for bonds, angles, and dihedrals
; -dihedsample ?
+
; -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
 
; -entropy : calculate vibrational entropy from normal modes
 
; -psf PSFfile CRDfile : use CHARMM PSF and CRD files to setup structure
 
; -psf PSFfile CRDfile : use CHARMM PSF and CRD files to setup structure

Revision as of 16:07, 31 July 2009

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 
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

Examples