Hello all, I have an isopeptide bond (between Lys site chain and carboxyl terminal of Gly) in my system and I defined this with specbond.dat and additional residue types and I edited .rtp files using Amber ff. Although I have this bond at the beginning (before pdb2gmx), it looks I need to add additional description for this bond (between two different chains) at the topology definition. How can I define it? (please see the picture, this is after energy min.)
serdar <http://gromacs.5086.n6.nabble.com/file/n5005445/isopep.png> -- View this message in context: http://gromacs.5086.n6.nabble.com/additional-bond-description-isopeptide-bond-between-two-chains-tp5005445.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
