[gmx-users] Problem wih Fe-S cluster

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 25 10:06:13 CEST 2009

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!



On Thu, Jun 25, 2009 at 7:55 AM, subarna
thakur<thakur.subarna at 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
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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