[gmx-users] pdb2gmx

[Justin Lemkul]

On 8/19/16 10:52 AM, amitbehra at chemeng.iisc.ernet.in wrote:
> Hello users,
> I am using pdb2gmx on a protein.
> Fatal error:
> Residue 1 named LYS of a molecule in the input file was mapped
> to an entry in the topology database, but the atom N used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> ATOM      1  N   LYS     8      59.565  44.696  51.226  1.00  0.00
>   N
> 0.00           H
> ATOM     19  NZ  LYS     8      62.201  50.111  51.767  1.00  0.00
>   N
>
> These are N atoms in my LYS . Can anyone point out what the problem.
>

Please provide your exact pdb2gmx command and the full screen output.

-Justin

-- 
==================================================

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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