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

Sotirios Dionysios I. Papadatos si.papadatos at edu.cut.ac.cy
Tue May 26 09:36:28 CEST 2015

OK, thanks but now I have a question what is the utility of a molecule.itp. You could just add the parameters from the beginning in ffbonded, nonbonded, atomtypes etc. Now it feels like I have to do double the work. 
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Monday, May 25, 2015 7:34 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Error using grompp - atomtype not found

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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