VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon May 07 2007 - 20:40:47 CDT

Hi Stephen,
are you using the text mode or gui interface? And which version of VMD?
All of your lipids have resname LIP, rather than POPC, and thus aren't
compatible with the topology files you're using. You should be getting a
message to that effect in either case. If you change all the residue
names to match the topology files things should work ok.
Best,
Peter

Stephen M. Dutz wrote:
>
> Hi all,
>
> I have been struggling with generating a psf file for the following
> POPC membrane pdb
> (http://www.lrz-muenchen.de/~heller/membrane/fluid.pdb.Z
> <http://www.lrz-muenchen.de/%7Eheller/membrane/fluid.pdb.Z>), courtesy
> H. Heller. I have been using AutoPSF with the topology files
> par_all22_prot.inp and par_all27_lipid.prm. It will generate a
> “temporary” pdb and psf and load them into VMD for visualization.
> However, the “temporary” files lack a significant amount of water
> molecules that are present in the initial pdb file (the total atom
> number decreases from ~27k to ~13k). Additionally, if I try to reload
> the temporary psf and pdb it will not do so. Any suggestions or ideas
> at what I might be doing wrong?
>
> Thanks is advance,
>
> Stephen
>