[gmx-users] select atoms of a particular zone, through trajectory
jalemkul at vt.edu
Sat Apr 9 14:47:48 CEST 2016
On 4/8/16 7:59 AM, Mahboobe Sadr wrote:
> Dear users,
> I am trying to find out which water molecules are interacting with the
> ligand, in a protein-ligand simulated system and through the simulation
> time. Is there any way to find these molecules and extract a trajectory
> which includes these molecules plus my protein-ligand complex?
The selection can be made with gmx select, but you won't be able to write a
trajectory because it will be discontinuous (different number of atoms per
frame), which is not supported. But you can get index files corresponding to
which atoms match the criteria to export individual coordinate files.
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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