On 9/21/16 8:43 AM, Irem Altan wrote:

Is there a way to write out simulation results with trjconv such that the atoms 
are in the same order as in the input .pdb file with the same chain/atom names?

Trajectories are written in this order already. If you had chain information in the input coordinates, they will be incorporated into the .tpr file and you can produce a coordinate file with that information. No such information is ever stored in a trajectory (because things like atom names, residue names, etc are never stored there, anyway).



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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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