[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

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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