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Hello Olivier-- > In the script I have sent, I group the dimers backbones in order to avoid > the breaking of the symmetry. I if remove this condition, I have no more > warning on cycle links (except on a histidine), but the potentials bond, > angles and improper are still 0. Though those warnings are annoying, they > are probably not linked to my issue. The problem stems from a bug in regularize.addUnknownAtoms (which is fixed in the upcoming release). A workaround for now, is to add an additional protocol.initNBond() after regularize.addUnknownAtoms(). My apologies for the problem, and good luck with your project. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkwqFmMACgkQPK2zrJwS/lbKSwCeKCJXYqStpMEeMuy0MTsBH9JJ 9iIAnAoEH/0nO7p34Ovi5/GMDWFpvZQJ =kOtY -----END PGP SIGNATURE-----
