> You said before: > > "> > 5. What does your .top look like? (does it list the organic molecule > > > only once in the [ molecules ] section?) > > Only once." >
OK. We misunderstood one another. I meant "CIP is mentioned only once" = "one string with CIP molecules number". So this entry was not really duplicated. > Does this mean you have only one solute? Or that you have only one entry for > solute, which you then have multiple molecules of in the system? There > certainly can be confusion if you aren't describing your system clearly. > > The reason for asking is that the problematic atom numbers (which are greater > than 42, as Chris pointed out) would indicate one of two possibilities: > > 1. CIP is present multiple times, and one of those molecules (at least) is > having a problem. YES. I just need to find out why the problem appears. -- 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/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/mailing_lists/users.php