[gmx-users] genion problem with topology

gangotri dey holyriver6 at gmail.com
Tue Jul 3 19:47:45 CEST 2018

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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