Hi Justin, Sorry for the late reply. Haven't had a chance to look at this yet. Could you post your output files or compare the contents of yours to mine? I chose Gromos 54a7 as my forcefield with the SPC water model. (command line is gmx pdb2gmx -f 1aki.pdb). I'd like to know if this is a cosmetic issue or if something else is going on.
My files can be found here: https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0 Thanks Dries On 1/20/16 3:48 AM, Dries Van Rompaey wrote: >* Hi Justin and Marco, *>>* Thanks for your reply. I get this behaviour when I specify the default NH3+ *>* and COO- termini through -ter, as well as when I don't use the -ter flag. *>* Selecting the COOH terminus type removed the warning for the C-terminus, *>* but selecting the NH2 terminus type did't remove the warning for the *>* N-terminus. That's not a very physiological state, however. *>>* Can anyone replicate this error? *> I can't trigger the same with 5.1 or with current git master. Try from a fresh install and make sure no one has messed with your force field files. -Justin -- -- 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.
