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

Justin Lemkul jalemkul at vt.edu
Fri Jul 3 17:47:29 CEST 2015

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 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


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