Re: Create psf file

From: Asma el-magboub (
Date: Mon Jun 22 2015 - 18:43:13 CDT

Hello Siska,

First you have to match the name of molecule in both files, in your pdb
file the name of molecule is TAR while in toppar file it is MOLECU, so
change it to TAR to match.
Second split toppar.txt to top.txt and par.txt then in top.txt rename all
atoms in third column to C , O, H, ....etc. VMD can't read these atom types
(for example change CG2R61 to C, HGR61 to H, OG2D2 to O, etc) but when psf
file is generated you have to return these names to the original.
Just do these editing stuff and it will work.


On Sat, Jun 20, 2015 at 3:56 PM, Fransiska Kurniawan <> wrote:

> Dear NAMD user,
> I want to ask, how to create psf file if we have ligand file and already
> get the topology and parameter file from cgenff?
> I tried to use the automatic psf builder in VMD, it is failed. then I
> tried to make the psf file manually (using the script) and it also failed.
> Here attached the pdb file of my ligand and also the topology and
> parameter file that I got from cgenff.
> Anyone can help me please?
> Thank you for your help.
> Regards,
> Siska

*Asma S. El-MagboubM.Sc. Pharmaceutical Sciences*
*PhD Student*
*Dr. Ian Haworth Laboratory*
*Department of Pharmacology and Pharmaceutical SciencesSchool of
Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089*
*Email: <> /

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