[Xplor-nih] Metal-cluster

[Hongyan Li]

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:

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> 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
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