[gmx-users] Topology for ready-made membrane protein system
anu80125 at gmail.com
Mon Jul 6 13:05:20 CEST 2015
Do I need to add lipid topology manually, if I use Charmm36 force filed
that have protein and lipid parameters together?
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
>> system ( contains lipids, protein, water and ions) with some
>> 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
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users