Hi gromacs users, In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate triple bonds between C and S and 3 single bonds between S and 3 O atoms.
I added these commands in specbond.dat to resolve the issue NAF S 6 NAF O4 2 0.3 NAF NAF NAF S 6 NAF O5 2 0.3 NAF NAF But, it didn't solve my problem. Any suggestion for solving this problem? Regards, Ehsan -- 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
