On 4/4/13 3:56 AM, Parul tew wrote:
Dear GMX users,
I am working on a protein which I want to simulate in a lipid bilayer
environment (POPC) and want to use OPLS force field for the same. I have
previously rum the membrane protein simulations using 43a6 force field with
the help of justin's tutorial which had run quite fine. But I am having
problems for generating a topology file for OPLS ff to incorporate both
lipid and protein's topology. As the OPLS ff only contains atomtypes in
ffoplsaanb.itp file only contains the atom types, I am not able to make out
what necessary changes to follow to generate a topology file incorporating
both lipid and protein.
lso the POPC lipid.itp (acquired from university of calgary website) is
quite different from the default ffoplsaanb file so I was wondering if
there is source to get the OPLS force field parameters for lipids.
There are many papers that describe modifications of the Berger lipids (the
parameters distributed by Tieleman) and an OPLS representation of the protein.
Otherwise, there are also numerous reports of OPLS parameters for lipids, for
instance:
dx.doi.org/10.1021/ct900086b
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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