[gmx-users] PDBs for mixed lipid bilayer/membrane
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 2 20:08:16 CEST 2008
Volker Wirth wrote:
> Hello list,
> first of all, my question in short: Does anyone know a source for
> PDB-files of mixed membranes (such as DMPC/DMPS or so)?
> And here more info:
> Within my diploma thesis I want to simulate a protein (ca. 20
> residues) interacting with a lipid bilayer (not a transmembrane
> protein). Besides the probably normal challanges in starting up with
> GROMACS, I need your help with a special problem:
> As a source for one-component bilayer pdb's (containing DOPC, SDPC,
> DMPC, DPPC and POPC) I found
> and maybe one could do fancy (protein insertion-) things using the
> membrane builder of
> but to get closer to reality (and to be able to compare simulation
> results with experiments) one might prefer a mix of different lipids
> (e.g. DMPC, DMPS, DMPG, at least anything like **PC, **PS, **PG or
> anything like that). Here is my problem, because I can't find any
> sites that offer such pdb files.
Right, I don't know of any either! One place to check would be Mikko
The site advertises a raft configuration, but it is not online. Perhaps
contacting the corresponding author of the related paper might be useful.
The only report of a simple binary mixture of lipids is the following
Leekumjorn, S. and Sum, A.K. (2006) Biophys. J. 90: 3951-3965.
They might also make their DPPC/DPPE configuration available.
As far as anything more complex, I haven't seen it, although that
doesn't mean it's not out there. I (and probably others on this list)
would also be interested in hearing back if you come across any other
> Is there someone out there who knows more or even has experience in
> simulations like that? A similar example would help me with this, too.
> Thanks a lot in advance, I hope I can share my knowledge some other time, too
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users