[gmx-users] Using x2top and grompp

Justin Lemkul jalemkul at vt.edu
Fri Sep 30 12:02:54 CEST 2016

On 9/30/16 5:34 AM, Devon wrote:
>> My goal is to get a topology.tpr and trajectory.xtc in those file formats.
>> I’m starting off with .pdb, .xyz, and .gro files of an experimentally
>> determined crystal structure. The crystal contains two kinds of molecules
>> that interact via halogen bonding. i do not want to run these molecules in
>> a solvent. i produced a topology.top file using x2top but when i tried to
>> use grompp to produce a tpr and i only got an mdout.mdp. what am i doing
>> wrong? I’m willing to start over completely. I also need to know how to run
>> my crystal without a solvent.

If grompp failed, it will give clear errors.  You haven't shared any of that 
information, so there's nothing anyone on this list can do.

If you don't want solvent, don't add any.  There's no requirement or special 
tricks about having a solvent.



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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