[gmx-users] genion problem with topology
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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users