|
|
Difference between revisions of "genPSF.pl"
From MMTSB
| (2 intermediate revisions by the same user not shown) | |||
| Line 6: | Line 6: | ||
== Description == | == Description == | ||
| − | Generate a protein structure file (PSF). This is often useful when dealing with large PDB files. | + | 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 == | ||
| Line 13: | Line 13: | ||
; -par CHARMMparams : use specified [[CHARMM_Parameters]] | ; -par CHARMMparams : use specified [[CHARMM_Parameters]] | ||
; -crdout file : generate coordinate file (CRD) | ; -crdout file : generate coordinate file (CRD) | ||
| − | ; -xplor : generate a PSF file | + | ; -xplor : generate a PSF file in XPLOR format (this format is needed as input to NAMD) |
; -log file : generate a CHARMM log file | ; -log file : generate a CHARMM log file | ||
; -cmd file : generate a CHARMM input file | ; -cmd file : generate a CHARMM input file | ||
| Line 19: | Line 19: | ||
== Examples == | == Examples == | ||
| − | <mmtsbToolExample cmd="genPSF.pl" set="/ | + | <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
...