[gmx-users] Problem in using pdb2gmx to generate top file

[Justin Lemkul]

On 1/8/16 5:46 AM, 张敏华 wrote:
> Hi everyone, I encountered a problem when I using pdb2gmx to convert a pdb file into gro and top file. The system give me a fatal error message as following:
>
> Fatal error:
> Residue 145 named LYS of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CG used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> But the 145 residue is LEU actually, and the sidechain of this residue is OK, I replaced this residue with ALA, ARG or LYS but the error message remains. So does anyone know the cause and help me to solve this ?
>

pdb2gmx uses its own internal residue numbering.  You must have a lysine 
somewhere with an incomplete side chain (a very common problem).  You'll need to 
fix the structure using e.g. SwissPDBViewer or some other modeling software 
before running the structure through pdb2gmx.

-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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