[gmx-users] md simulation by gromacs.

[Justin Lemkul]

On 10/28/16 2:50 PM, maria khan wrote:
> Hello dear  gromacs users..
> I am running simulation for protein ligand complex that are Glutamate
> racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in
> residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting
> atoms.For a hydrogen, this can be a different protonation state, or it
> might 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."for making pdb2gmx and it
> doesnt form topology file.
> where am i doing wrong.
> kindly help me out.

I answered this yesterday:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-October/109172.html

-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

==================================================