VMD-L Mailing List
From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Aug 18 2011 - 07:06:32 CDT
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Dear VMD users,
Last week, in the manuscript "Structure and Dynamics of the
Membrane-Bound Cytochrome P450 2C9"
(http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002152),
we have published a protocol to convert coarse grained POPC lipids to
atomistic representation (Protocol S2 in the paper).
This is implemented for VMD (+AMBER) and uses the published GAFF force
field for POPC lipids.
If there is interest in this protocol, one could imagine developing it
into a plugin for VMD and/or extending it to other atomistic force
fields for lipids.
If anybody is interested in using this protocol, in its extension to
other atomistic force fields (CHARMM would be an obvious choice), or in
converting it into a VMD plugin, please give it a try and let me know
about your experiences.
Best wishes
Vlad
-- Dr. Vlad Cojocaru Max Planck Institute for Molecular Biomedicine Department of Cellular and Developmental Biology Roentgenstrasse 20 48149 Muenster, Germany tel: +49-251-70365-324 fax: +49-251-70365-399 email: vlad.cojocaru[at]mpi-muenster.mpg.de
- Next message: Mert Gür: "How can I draw secondary structures if I only have the carbon alpha coordinates"
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