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 <holyriv...@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* > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.