RE: Create psf file

From: Raed Ahmed Abdelsalam Shalaby (
Date: Mon Jun 22 2015 - 05:54:32 CDT

First you need to split the file that you got from cgenff into ligand_top and ligand_param. (attached is ligand_top)

To generate the psf file you need the following (in one directory):

pdb of the protein (protein.pdb)
pdb of the ligand (tartrazine.pdb)
topology of the protein (top_all27_prot_lipid.inp)
pgn file, a txt file written as follows:

package require psfgen
topology ligand_top
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment A {pdb tartrazine.pdb}
coordpdb tartrazine.pdb A
segment B {pdb protein.pdb}
coordpdb protein.pdb B
writepdb complex.pdb
writepsf complex.psf

Save the file (example.pgn) in the same directory, go to this directory and run: psfgen example.pgn

It works with me

Raed A. Shalaby
Research Assistant,
Pharmaceutical Sciences Section
College of Pharmacy
Qatar University, Doha, Qatar<>
From: [] on behalf of Fransiska Kurniawan []
Sent: Sunday, June 21, 2015 1:56 AM
To: NAMD List
Subject: namd-l: Create psf file

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.


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