[MMTK] NMA

[Konrad Hinsen]

On Mar 17, 2006, at 14:57, vanitha at cs.wisc.edu wrote:

> Thanks a lot! The only thing though is that I have three objects,
> 1) Co-crystallized complex containing the receptor and ligand
> 2) Unbound structure of ligand
> 3) Unbound structure of receptor

That makes no difference in principle, you can use the same approach  
for any number of objects.

> I want to use the normal modes of the unbound structures to refine the
> structure of the complex. The procedure you outlined assumes that I'm
> going to use the normal modes of the ligand and receptor from the  
> complex.

Formally, yes, but physically not. A complex that consists of non- 
interacting items (because of the distance) is physically equivalent  
to a collection of unbound structures.

Konrad.
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Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: konrad.hinsen at cea.fr
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