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

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

Examples

nmaCHARMM.pl -minimize 10000 -par dielec=rdie,epsilon=4 -modes 20 -xtract mode 1vii.exp.min.pdb
minimizes the input structure and calculates the 20 lowest normal modes. The frequencies are written to standard output, the modes are written to files mode.NN. Note that the first six modes are rigid body translation/rotation.

1 -0.392097 99.995286
2 -0.000028 100.000000
3 0.000015 100.000000
4 0.000027 100.000000
5 0.197511 99.986227
6 0.377622 99.987526
7 3.805419 0.021347
8 4.272848 0.007178
9 6.516272 0.000252
10 8.586901 0.000691

...