From: Peter Freddolino (
Date: Fri Apr 03 2009 - 15:54:42 CDT

Hi Katherine,
if you download the charmm forcefield distribution from the MacKerell
lab website (, you
can find a variety of model compounds in the stream directory that may
have what you're looking for.

Katherine Parra wrote:
> Dear vmd community:
> I'm using psfgen to generate a psf file of a protein with three ligands.
> These ligands are: acetate ion, formic acid and glycerol.
> The topology file I'm using is the top_all27_prot_lipid.inp
> The problem I'm having is that I don't know and I don't find the right
> names for these ligands in the top file.
> My question is should I use another top file?
> Thanks in advance.
> KParra