[gmx-users] genion problem with topology

[Justin Lemkul]

On 7/3/18 1:47 PM, gangotri dey wrote:
> Dear all,
>
> I have replaced one water molecule in the solvent with a Cl atom using
> genion. My syntax is as follows:
>
> gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1
> -nname CL
>
> I have generated the ions.tpr using the ion.mdp file as in the tutorial
> from Bevan group.
> I see that the topol.top adds CL at the end under [molecules] but when I
> try to minimize the geometry using the new solvate.gro file the error as
> given as
>
> ERROR 1 [file topol.top, line 37]:
>    No such moleculetype CL
>
> I do not understand how I can rectify the problem. Can someone help?

The ion [moleculetype] definitions are all handled by ions.itp in the 
parent force field. Make sure you're following the force field's naming 
convention and make sure #include "whatever.ff/ions.itp" is in your .top 
file (it should if produced by pdb2gmx).

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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