[gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?

Justin Lemkul jalemkul at vt.edu
Wed Aug 26 19:51:21 CEST 2015

On 8/26/15 1:47 PM, Barnett, James W wrote:
> Look into the pull code. You'll want to choose two groups (one for the ligand, one for the binding site), and one coordinate with those groups where the pull rate is not zero (negative rate to bring them together, positive rate to pull them apart).

And if the purpose is just some cute movie that is not necessarily 
scientifically relevant (shakes head sadly), restrain the protein in some way to 
avoid the inherent problem of "hitting a moving target."


> --
> James “Wes” Barnett, Ph.D. Candidate
> Louisiana Board of Regents Fellow
> Chemical and Biomolecular Engineering
> Tulane University
> 341-B Lindy Boggs Center for Energy and Biotechnology
> 6823 St. Charles Ave
> New Orleans, Louisiana 70118-5674
> jbarnet4 at tulane.edu
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Victor Ma <victordsmagift at gmail.com>
> Sent: Wednesday, August 26, 2015 12:31 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?
> hello all
> I got a urgent request to make a MD movie for pulling the ligand out of the
> binding site/or the ligand flying into the pocket . I feel like i need to
> run something like steered md, which I've never done before. So can anyone
> please suggest a quick and "dirty" way to generate such a movie?
> Thank you!!
> Victor
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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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