[gmx-users] 54a7 force field & pdb2gmx & topology database

[Justin Lemkul]

On 3/30/16 8:16 AM, Brett wrote:
> Dear All,
>
> When I work with pdb2gmx for force field 54a7, I meet the following
>
> "WARNING: Residue 54 named ILE of a molecule in the input file was mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed".
>
> Why you please let me know how to localize the topology database and how to localize ILE in the topology database , so that I can compare the atom O with that in my input pdb file, for fix of my pdb file?
>

The error is explicit - you are missing an O atom (backbone carbonyl oxygen) in 
your coordinates.  You need to fix any missing atoms or residues.

-Justin

-- 
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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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