[gmx-users] select atoms of a particular zone, through trajectory

[Justin Lemkul]

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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