VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Apr 03 2009 - 15:54:42 CDT

Hi Katherine,
if you download the charmm forcefield distribution from the MacKerell
lab website (http://mackerell.umaryland.edu/CHARMM_ff_params.html), you
can find a variety of model compounds in the stream directory that may
have what you're looking for.
Best,
Peter

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