Rebeca García Fandiño wrote:
Hello,
I would like to simulate a membrane + protein system using the OPLS
force field for both, the protein and the membrane. I have looked for a
previous equilibrated membrane simulated using the OPLS force field, but
I did not find it.
Please, does anybody knows where I could find a membrane simulated with
the OPLS force field?
I've never seen one either. The Berger parameters (commonly used) are based in
part on OPLS parameters, and as such, Chris Neale has posted a nice procedure
for modifying the Berger parameters (present at Tieleman's site as lipid.itp)
such that they can be used in conjunction with an OPLS representation of your
protein:
http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html
Recent literature (from Tieleman's group) has suggested that this is a more
accurate representation of protein-lipid interactions than the classic
Gromos+Berger representation that is quite common in the literature.
If you're desperate for an OPLS bilayer, you may have to generate it yourself.
-Justin
Thank you very much for your help.
Best wishes,
Rebeca García
Parc Cientific de Barcelona
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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