[gmx-users] error in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Sun Apr 17 18:10:33 CEST 2016

On 4/17/16 12:05 AM, Shahla Omidi wrote:
> ​hello
> I want to simulate my protein with charmm36, and I used gromacs505 for this
> I took this error with pdb2gmx
> "Residue 1 named PRO of a molecule in the input file was mapped
> to an entry in the topology database, but the atom N used in
> an interaction of type improper in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed."
> residue 1 is not "proline" in my protein and I dont know what I should do to solve this problem
> could you help me?

Please provide your full command and the entire screen output so we can see the 
selections and how pdb2gmx is parsing the chains.



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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