[gmx-users] genion problem with topology

Justin Lemkul jalemkul at vt.edu
Tue Jul 3 20:51:31 CEST 2018

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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