[gmx-users] Error in .rtp Entery

[Justin Lemkul]

On 7/20/16 8:12 AM, Sanjay Singh wrote:
> 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:Residue 37 named
> VAL of a molecule in the input file was mapped
>
> to an entry in the topology database, but the atom CG1 used in
>
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed,while the position of VAL is 36
> (52) in 1CF7.pdb file
>

pdb2gmx uses its own internal numbering.  But you have an incomplete valine 
somewhere.  Check the header of the PDB file for "MISSING" lines, which should 
always be the first step wen preparing a system.  Address any missing atoms or 
residues, and then try pdb2gmx again.

-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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