VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Aug 18 2011 - 07:06:32 CDT

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