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
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--
************************************************
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
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