Hi Charles, 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.
Olivier 2010/6/24 <Charles at schwieters.org> > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Olivier-- > > > If I do not apply the patch, the enery output is usual with no zero > > values. I indeed have some warnings, all on this model : > > > > AT_Build::buildNode: cycle link found between atoms 770 LYS 48 C and 774 > GLN > > 49 N > > removing bond. > > AT_Build::buildNode: cycle link found between atoms 789 GLN 49 C and 791 > LEU > > 50 N > > removing bond. > > AT_Build::buildNode: cycle link found between atoms 808 LEU 50 C and 810 > GLU > > 51 N > > > > This is an IVM message, not related to energies- it would be a good idea > to understand the cycles, and to break them at an appropriate > place. However, to figure out your zero energy problem, I will need some > more information. If you are able to upload a complete working example > to http://nmr.cit.nih.gov/xplor-nih/download.cgi, that would be > easiest. > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAkwjWdoACgkQPK2zrJwS/lbp6wCfS1FDqu9Ew1BhQhhS7oeFdeXw > 238An2Ofelj3GDjtjkAod8BecJFT3gh7 > =P7WE > -----END PGP SIGNATURE----- > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20100626/8ed81db5/attachment.html
