Remove coordinates of ligand from .pdb file as you call coordinates of ligands two times first from .pdb file and second by putting drg.itp calling from .top file
On Sun, Oct 6, 2019, 9:30 PM Iman Katouzian <imanetern...@gmail.com> wrote: > Hello, > > I have simulated a protein-ligand file and produced the ligand file by > antechamber software using the Amber03 force field. All the stages in > Gromacs were performed correctly without any error however when I ran this > code : > > gmx grompp -f MDP/ions.mdp -c solv.gro -p topol.top -o ions.tpr > I encounter this error: > > Fatal error: > number of coordinates in coordinate file (solv.gro, 40906) > does not match topology (topol.top, 40950) > > I just performed my simulation many times but I could not pass this error. > > Thanks > > > > -- > > *Iman Katouzian* > > *Ph.D.** candidate of Food Process Engineering* > > *Faculty of Food Science and Technology* > > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* > -- > 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.