Hey, > The problem comes from the special linkage between PGL and whatever the > subsequent amino acid is - the amide is formed through the side chain. As > such, you will need to specify a special bond in specbond.dat before this > connectivity will be recognized. If this is successful, then the PHE should > no longer be recognized as a terminal residue and thus will not receive any > additional protonation.
That's not correct. Pyroglutamic acid is basically a proline with an oxy group due to formation of an intra-residue ester bond. There's no bond between the side chain and the next amino acid. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
