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

[Sotirios Dionysios I. Papadatos]

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

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

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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