Dear Charles, I used formatconverter to convert NOE format from Cyana to CNS, it works fine for my other protein without metal ions. I still believe that something wrong with PSF file. Since in the metal cluster, Cd-S distances and angles were fixed, but in this protein, for each Cd, both Cd-S distances and angles varied according to our Cyana structures and published structures.
I got Cd radius of gyration value from parameter files of CNS (ion.param), not sure where to get proper value. Best wishes, Hongyan Quoting Charles at Schwieters.org: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Hongyan-- > > > I have tried to build Cd-S clusters as you suggested before and then > > generate PSF file and to calculate structures using anneal.py script > > with constraints of NOE, RDC. I got many violations on RDC, Angel, NOE > > etc. The structures are bot correct when compared with that obtained > > from Cyana as well as those similar protein structures. Please see the > > attached file for the scripts I used. Any suggestions? > > > > Perhaps your distance restraints need to be converted from Cyana's > conventions - see Marius' post on this issue: > http://dcb.cit.nih.gov/pipermail/xplor-nih/2007-March/000574.html > > I can't see anything obviously wrong with the scripts, except that your > radius of gyration value is probably too large. > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> > > iD8DBQFGINX3PK2zrJwS/lYRAoQOAJ9KEGVdwyfPDKctVxfbLmPnDqjU1wCfUHB+ > 5Rp4s1Jsmc7DKxavhZCayW4= > =iG0q > -----END PGP SIGNATURE----- >
