> [Question 1] The topology file produced by pdb2gmx with Amber FF > (ffamber03, for example) looked different from what we used to obtain with > ffG43a1. > > No force constants were assigned in [ bonds ], [ angles ], [ dihedrals ], > etc.
That's because they're being read from ffamber03bon.itp by grompp when the time comes, according to the atom names/types. > [Question 2] In the RTP file of Amber FF, again no force constants were > assigned in [ bonds ], [ dihedrals ], etc., and [ angles ] was missing. > > Is it what it¡¯s supposed to be? pdb2gmx generates angles, pairs, exclusions, etc. based on the bonding connectivity and the defaults for the force field. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
