[gmx-users] Md simulation error

[Justin Lemkul]

On 10/27/16 2:03 PM, maria khan wrote:
> Hello dear gromacs users,
> i m running md simulation for protein ligand complex that are glutamate
> racemase and its inhibitor (KRH) bt it gives an error like "Atom HD1 in
> residue HIS 61 was not found in rtp entry HISB with 12 atomswhile sorting
> atoms.For a hydrogen, this can be a different protonation state, or itmight
> have had a different number in the PDB file and was rebuilt(it might for
> instance have been H3, and we only expected H1 & H2).Note that hydrogens
> might have been added to the entry for the N-terminus.Remove this hydrogen
> or choose a different protonation state to solve it.Option -ignh will
> ignore all hydrogens in the input."
> where am i doing wrong.

Your H nomenclature doesn't match the expectations of the force field.  pdb2gmx 
has suggested a fix, which you should probably use.  Or ask Google, who knows 
all about different tips and tricks, since this gets asked and answered frequently.

-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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