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Hi-- > > "PARRDR-ERROR: duplication of nonbonded entry CS2", or, > "PARRDR-ERROR: duplication of bond entry C3S8 HA", or, > "PARRDR-ERROR: duplication of angle C3S6 CSN2 C3S7" > It looks like a parameter file somehow got loaded twice. > I check the output pdb file and find that the rotatable bonds between > cysteine and the ring of MTSL are missing in the final structure. Is > this related to the above error reports? Maybe not, because it seems > these bonds are missing as well in the demo output. > Can you tell us which atoms are missing (by atom name)? I don't see missing atoms in the output of the shipped version of addAtoms.py. regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFD4K79PK2zrJwS/lYRAh2EAJwJdUaP3lHQTx5f56A5Uoma8680mgCcC9Cs 2AoYrR2502OBZmSzkPC8jP4= =VmDk -----END PGP SIGNATURE-----
