[gmx-users] on atomtypes
jalemkul at vt.edu
Thu May 12 17:45:59 CEST 2016
On 5/12/16 11:42 AM, Brett wrote:
> Dear Justin,
> You see, the ligand.itp contains the HS14 information as following,
> 34 NT 1 ADP N6 7 -0.859 14.0067
> 35 HS14 1 ADP H10 7 0.406 1.0080
> 36 HS14 1 ADP H11 7 0.419 1.0080
> But when I run
> gmx grompp -f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr,
> it told me the "Atomtype HS14 not found".
> Will you please show me the way to have the issue settled?
How did you generate the topology? It's using an atom type that is not present
in the parent force field, therefore you get an error. Normally, external
(non-GROMACS) sources of topologies will provide an augmented topology file that
has the new [atomtypes] in it. If not, then whatever you're doing is
incompatible with the parent force field you're trying to use.
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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