[gmx-users] Error using grompp - atomtype not found

Justin Lemkul jalemkul at vt.edu
Mon May 25 18:34:31 CEST 2015

On 5/25/15 11:08 AM, Sotirios Dionysios I. Papadatos wrote:
> Hi,
> I have made a molecule.itp, which is what I want to run MD calculations on. Meaning I couldn't produce it with pdb2gmx but I rather made a .top with vi editor.
> When I try to use grompp it says atomtype opls_XXXX not found.
> I have added all the needed atoms in atomtypes.atp of the ff I want to use. I should also mention that I used an existing atom in atomtypes and then the ones I added. Also I used grep to see if I made any spelling mistakes.

The .atp file is used only by pdb2gmx.  You need to add parameters in 
ffnonbonded.itp for any new atom types; this is what grompp is complaining about.



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


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