Re: [gmx-users] genion problem with topology
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.
Re: [gmx-users] genion problem with topology
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 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.
