Hi Ignacio, You can solve the problem creating an index file through make_ndx. In such a file you need a group called ACX. Then use the index.ndx in grompp.
Francesco 2012/2/6, Ignacio Fernández Galván <jel...@yahoo.com>: > Hi all, > > I have a system with a molecule called ACX plus water (molecules called > SOL), but when I try to use "ACX" as a group name in the .mdp file, grompp > says such a group does not exist: > > ------------------------------------------------------- > Program grompp, VERSION 4.5.5 > Source code file: readir.c, line: 1320 > > Fatal error: > Group ACX 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. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > However, the .top file is, I believe, correct, it contains these lines: > > [ moleculetype ] > ; Name nrexcl > ACX 3 > > and then [atoms], [bonds], etc. It ends with: > > [ molecules ] > ; Compound #mols > ACX 1 > SOL 2139 > > and that's not a problem. It's when I try to use ACX as a group name, as in: > > energy_grps = ACX > > that I get the error. What am I doing wrong? Is there any option I must > activate to enable using molecule names as groups? > > Thanks, > Ignacio > -- > 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 > -- Cordiali saluti, Dr.Oteri Francesco -- 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