VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue May 08 2007 - 18:19:12 CDT

Hi Stephen,
my guess is you're running into pdb formatting issues. When you change
LIP to POPC, you need to make sure that you actually change "LIP " to
"POPC" -- you can't change the column position of subsequent fields,
because the pdb is a column based (not space delimited format). You're
probably getting incorrect coordinates as a result. Likewise, because of
the column-based nature, that isn't resname POPCL, but rather, resname
POPC, chain L. Please see the pdb file format specs
(http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html) for
more information.
Peter

Stephen M. Dutz wrote:
> Hi Peter,
>
> Thanks for the help. I am using the GUI with version 1.8.5. I changed
> all the "LIP" resnames to POPC. When I then load the pdb, the lipids
> become packed into a narrow cube in the middle of the solvation layers.
> I looked at one of the other pdb's I've been running and it uses resname
> POPCL. Upon trying this resname the lipids were all cut up into
> individual atoms. Any ideas as to why this might be?
>
> Thanks again,
>
> Stephen
>
> -----Original Message-----
> From: Peter Freddolino [mailto:beakerbreaker_at_gmail.com] On Behalf Of
> Peter Freddolino
> Sent: Monday, May 07, 2007 6:41 PM
> To: Stephen M. Dutz
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: autoPSF with a POPC membrane
>
> 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
>>
>>