[gmx-users] genion problem with topology

Shrinath Kumar shrinath.kumar at ucdconnect.ie
Tue Jul 3 20:48:20 CEST 2018

What forcefield are you using? Check if CL is defined in your forcefield
(it's probably not, which is why you are getting the error). Each type
under [ molecules ] must have a corresponding [ moleculetype ] section
defined somewhere in your forcefield files.

On 3 July 2018 at 18:47, gangotri dey <holyriver6 at gmail.com> 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?
> *Thank you*
> *Gangotri Dey*
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