genPSF.pl

Usage

usage:   genPSF.pl [PDBfile]
         [-par CHARMMparams] [-crdout file]
         [-xplor]
         [-log file] [-cmd file]

Show source

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

...