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Difference between revisions of "genPSF.pl"
From MMTSB
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== Description == | == Description == | ||
+ | Generate a protein structure file (PSF). This is often useful when dealing with large PDB files and is needed when running with NAMD. | ||
== Options == | == Options == | ||
; -help : usage information | ; -help : usage information | ||
+ | ; -par CHARMMparams : use specified [[CHARMM_Parameters]] | ||
+ | ; -crdout file : generate coordinate file (CRD) | ||
+ | ; -xplor : generate a PSF file in XPLOR format (this format is needed as input to NAMD) | ||
+ | ; -log file : generate a CHARMM log file | ||
+ | ; -cmd file : generate a CHARMM input file | ||
+ | == Examples == | ||
− | == | + | <mmtsbToolExample cmd="genPSF.pl" set="test1"></mmtsbToolExample> |
+ | <mmtsbToolExample cmd="genPSF.pl" set="test2"></mmtsbToolExample> |
Latest revision as of 03:35, 31 July 2009
Usage
usage: genPSF.pl [PDBfile] [-par CHARMMparams] [-crdout file] [-xplor] [-log file] [-cmd file]
Description
Generate a protein structure file (PSF). This is often useful when dealing with large PDB files and is needed when running with NAMD.
Options
- -help
- usage information
- -par CHARMMparams
- use specified CHARMM_Parameters
- -crdout file
- generate coordinate file (CRD)
- -xplor
- generate a PSF file in XPLOR format (this format is needed as input to NAMD)
- -log file
- generate a CHARMM log file
- -cmd file
- generate a CHARMM input file
Examples
genPSF.pl -par blocked -crdout 1vii.crd 1vii.exp.pdb
generates a CHARMM PSF file for the given PDB structure with blocked termini. A CRD file is also written out.
PSF CMAP CHEQ 2 !NTITLE * TITLE * DATE: 7/30/ 9 23:34:53 CREATED BY USER: apps 605 !NATOM 1 PRO0 1 MET CAY 24 -0.270000 12.0110 0 0.00000 -0.301140E-02 2 PRO0 1 MET HY1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02 3 PRO0 1 MET HY2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02 ...
genPSF.pl -xplor 1vii.exp.pdb
generates a PSF file in X-PLOR format for the given PDB structure
PSF CMAP CHEQ 2 !NTITLE * TITLE * DATE: 7/30/ 9 23:33:42 CREATED BY USER: apps 596 !NATOM 1 PRO0 1 MET N NH3 -0.300000 14.0070 0 0.00000 -0.301140E-02 2 PRO0 1 MET HT1 HC 0.330000 1.00800 0 0.00000 -0.301140E-02 3 PRO0 1 MET HT2 HC 0.330000 1.00800 0 0.00000 -0.301140E-02 ...