VMD-L Mailing List

From: Stephen M. Dutz (smdutz_at_csupomona.edu)
Date: Mon May 07 2007 - 19:37:25 CDT

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),
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