Dear Charles, Thanks for your advice. I don't know how to vary Cd-S distances and angles when generating PSF file. Any suggestions? Best wishes, Hongyan
Quoting Charles at Schwieters.org: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Hongyan-- > > > 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. > > > > you might do a survey of the pdb to find the observed range of these > bond lengths and angles. You are correct that you should allow the values > to vary in this structure if they are not found to be constant. > > > I got Cd radius of gyration value from parameter files of CNS > > (ion.param), not sure where to get proper value. > > if the selection you specify in initCollapse is globular (it should be), > then the default Rg it calculates should be reasonable. > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> > > iD8DBQFGI4SLPK2zrJwS/lYRAo3BAJ9WiBJ6uwiZGKjo4LAuwASxAOT/XACfennz > MKp4ugdoKf6bvvEKMimAFbA= > =mbu0 > -----END PGP SIGNATURE----- >
