[gmx-users] PDBs for mixed lipid bilayer/membrane

Jochen Hub jhub at gwdg.de
Thu Jul 3 08:32:17 CEST 2008

I had a similar problem some time ago and I didn't find an easy 
solution. So, what you could also do:

Take a single lipid molecule of each lipid component that you wand to 
place in the membrane. Use the Sculpting-Wizard of PyMol to pull on the 
atoms until the lipid is stretched (no tilted chains  etc.) Then write a 
litte python/pearl/bash script which places a number of lipids of each 
kind in a random fashion on a grid (e.g. 8x8 lipids per monolayer). The 
lipids need to be streched to avoid overlaps at the chains. Then add 
water (genbox) and equilibrate the system carefully, at least for 
10-20ns. Better more.

Contact me if you don't know how to write such script. I should find my 
script somewhere.

Hope that helps.

Cheers, Jochen

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
>    http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>    http://persweb.wabash.edu/facstaff/fellers/
>    http://www.lrz-muenchen.de/~heller/membrane/membrane.html
>    http://www.apmaths.uwo.ca/~mkarttu//downloads.shtml
> and maybe one could do fancy (protein insertion-) things using the
> membrane builder of
>    http://www.charmm-gui.org/
> 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.
> 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
> Volker
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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
> .

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

More information about the gromacs.org_gmx-users mailing list