Hi,
I made myself a force field for an organic polymer using a terminology/syntax similar to amino acids, so that i can make topoly files directly from pdb files using pdb2gmx. This worked nicely up to gmx-4.6.5, but when trying 5.0 pdb2gmx complains about not finding particular atoms in a pdb file, although they are there (only in the neighbouring residue), and then grompp gives up because it believes to find double entries in a angle or dihedral because the atom names in neighbouring resiues are identical. e.g. there's an entry in the angle section of resiue 2: "-C2 C1 C2" the first atom is in residue 1 the second and third are in residue 2 (as indicated by the minus sign) but pdb2gmx/grompp believe that all three names refer to atoms in residue 2 and thus grompp complanes about a duplicate atom and givbes up ... Is this something that was changed in 5.0 on purpose? cheers michael =============================== Why be happy when you could be normal? -- 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.
