[gmx-users] Fatal error: Residue 'GTP' not found in residue topology database

Justin Lemkul jalemkul at vt.edu
Mon Aug 31 13:32:32 CEST 2015

On 8/31/15 1:31 AM, Raag Saluja wrote:
> Yes,I did, Mark. Thanks! But I don't need GTP. The pdb file just shows a
> GTP-binding site. Can I get rid of this somehow? Or else, how may I get the
> .pdb file for GTP?

Your .pdb file also contains GTP, if pdb2gmx is complaining about it.  If it's 
not scientifically relevant to you, delete it from the .pdb file and run pdb2gmx 
again.  If it is relevant, you'll have to develop a topology for it, which is 
straightforward to do for most force fields (since all the building blocks are 



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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