Hi Subarna,
If you just want to retain the structure of the cluster it doesn't
matter too much. It may be good to average values from different
structures, though. HOWEVER, an FeS cluster is a catalytic site, which
probably has fancy electronic properties, which may well affect the
behaviour of the surrounding protein. If you are interested in the
protein dynamics, you want to describe it properly. Doing so requires
proper parameterization, ergo performing quantum mechanical
calculations with validation against experimental data, ergo doing a
lot of work. This is not something for a lazy Sunday afternoon!
Cheers,
Tsjerk
On Thu, Jun 25, 2009 at 7:55 AM, subarna
thakurthakur.suba...@yahoo.co.in wrote:
Hi everyone
I am facing a problem with derivation of parameters of Fe-S cluster in a
protein.Can anybody please tell me for deriving a parameters do I have to
consider the co-ordinates of a typical fe-s cluster as there in Protein Data
Base (PDB) or the co-ordinates of the Fe-S cluster present in my protein of
interest.
Subarna
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
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