[gmx-users] Topology for ready-made membrane protein system

[Mark Abraham]

Hi,

You need a topology for each moleculetype, and parameters for the
interactions they require. These are separate issues.

Mark

On Mon, 6 Jul 2015 13:05 anu chandra <anu80125 at gmail.com> wrote:

> Dear Justin,
>
> Do I need to add lipid topology manually, if I use Charmm36 force filed
> that have protein and lipid parameters together?
>
> Thanks
> Anu
>
> On Fri, Jul 3, 2015 at 4:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/3/15 7:56 AM, anu chandra wrote:
> >
> >> Dear Gromacs users,
> >>
> >> I am working with membrane proteins. I have generated the
> >> membrane-protein
> >> system ( contains lipids, protein, water and ions) with some
> >> specification.
> >> For eg.,  I have positioned  few ions and water molecules at particular
> >> location using some in-house programs. Now, I would like to generate
> >> topology for the my system in order to run MD using Gromacs. Since my
> >> system is ready-made, I cant follow the methodology adopt by Gromcas
> >> membrane-protein  tutorials.
> >>
> >> Hence, can anybody suggest me a way to generate Gromacs inputs files for
> >> such ready-made membrane-protein systems?
> >>
> >>
> > Process the protein with pdb2gmx and add an #include statements for the
> > lipid topology.  Then modify [molecules] to account for what's actually
> in
> > the system.  Water and ion topologies will automatically be #included in
> > the .top written by pdb2gmx.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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