Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]).
On 2012-03-07 05:13:11PM +0000, Lara Bunte wrote: > Hi > > I create a file pr.mdp for equilibrating the water around my molecule and > used after that the command > > grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr > > And I got tthe error: > > Fatal error: > Group protein not found in index file. > Group names must match either [moleculetype] names > or custom index group names,in which case you > must supply an index file to the '-n' option of grompp. > > Could you explain that error to me please? How to fix it? > > Greetings > Lara > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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