[gmx-users] grompp does not find atomtype

Justin Lemkul jalemkul at vt.edu
Thu Jun 26 19:50:24 CEST 2014

On 6/26/14, 1:47 PM, Dawid das wrote:
> Dear Gromacs experts,
> I have succesfuly put new atom types into force field expression.
> I have managed to run pdb2gms, editconf and genbox.
> But when I try
> grompp -f minimize.mdp -c mCherry7-solv.gro -p mCherry7.top -o minimize.tpr
> then I get an error saying that one od my newly inctroduced atoms is not
> found... :|
> Fatal error:
> Atomtype MH41 not found
> I have checked all of the files once again and it is in atomtypes.atp and
> aminoacids.rtp. Also all of the defined parameters use names MH41, MH42 and
> MH43.
> Why do I get this error?

atomtypes.atp is only read by pdb2gmx.  You need to add parameters for your new 
atomtypes in ffnonbonded.itp.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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