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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
