[gmx-users] help with "interaction of type atom in the topology database, but an atom of that name was not found in residue" error

Justin Lemkul jalemkul at vt.edu
Wed Jan 8 15:45:54 CET 2014

On 1/8/14, 9:39 AM, paulxie wrote:
> Thanks for the answer! However, when I run the command below:
>   grompp -f ions.mdp -c xxx_solv.gro -p xxx_topol.top -o xxx_ion.tpr
> It keeps showing the error message:
> Fatal error:
> Topology include file "ff_dum.itp" not found
> Is there a possible way I can skip or not include the file 'ff_dum.itp'?

Remove it from whatever file is #including it.  Probably something in the force 
field distribution itself.  It was designed for an older version of Gromacs, so 
some kinks may need to be worked out.



Justin A. Lemkul, Ph.D.
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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