[gmx-users] Problem with generating topology file for OPLS force field for membrane protein simulation
jalemkul at vt.edu
Thu Apr 4 10:20:48 CEST 2013
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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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