[gmx-users] on atomtypes

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================