Re: Joining PSF Files

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Tue May 24 2011 - 09:04:53 CDT

Create a PDB file for each molecule.

Build with a TCL script. Each entry in the TCL script corresponds to a
particular molecule.

psfgen <<ENDMOL
topology top_all27_prot_lipid.inp

segment TIP3 {
 pdb water.pdb
 auto none
 first none
 last none
 }

 segment CAL {
 pdb cal.pdb
 auto none
 first none
 last none
 }

 segment CLA {
 pdb cla.pdb
 auto none
 first none
 last none
 }

#Read coordinates
coordpdb water.pdb TIP3
coordpdb cal.pdb CAL
coordpdb cla.pdb CLA

writepsf setup.psf
writepdb setup.pdb

PAUL NEWMAN wrote:
> Dear NAMD Users,
>
> I am building the psf file of two different molecules. I was wondering
> if there is a way to join then into one file for the simulation in NAMD.
>
> Thanks again for your help
>
> --
> Cheers,
>
> Paul
>
>

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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