Not sure - perhaps if you've edited this file by hand (or in an inappropriate editor) there's a tab-vs-space issue, or missing line ending on the final line.
Mark On Fri, Feb 8, 2013 at 7:40 PM, Asma Mushtaq <ashima.as...@gmail.com> wrote: > Dear All, > > > > I need to add 6 CL ions to make the system neutral but when I type the > command line > > > > genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 > > > > and choose group 15 (SOL), the error is > > > > Fatal error: > > No line with moleculetype 'SOL' found the [ molecules ] section of file > ‘topol.top’ > > > > but when I check the ‘topol.top’ file I found there are 24504 SOL molecules > present. > > > > My topology file looks like this > > > > ; Include water topology > > #include "amber99sb.ff/tip3p.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcx fcy fcz > > 1 1 1000 1000 1000 > > #endif > > > > ; Include topology for ions > > #include "amber99sb.ff/ions.itp" > > > > [ system ] > > ; Name > > Protein > > > > [ molecules ] > > ; Compound #mols > > Protein_chain_A 1 > > ATQwild 1 > > SOL 24504 > > > > > > Please let me know how to rectify the problem > > > > > > regards, > > > > Ashima > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists