Konrad Hinsen konrad.hinsen at cea.fr
Fri Mar 17 12:58:34 CET 2006

On Mar 17, 2006, at 3:28, vanitha at cs.wisc.edu wrote:

> I have another question regarding Normal Mode analysis.
> I have a bound complex (ligand and receptor pair) that I've added to a
> universe. I now need to compute the normal modes for the respective
> unbound versions of these proteins and add the displacements along  
> these
> normal mode s to the configuration of the original complex. In other
> words, the free parameters are now the amplitudes of the normal  
> modes that
> further refine the structure of the complex.
> I am running into an interesting situation here:- I add the complex  
> to a
> universe defined by the all-atom Amber Force Field, and I add the  
> unbound
> structures to a different universe defined by a Deformtion Force  
> Field.
> Would I end up with a problem if I add the displacement along the  
> normal
> modes computed from one universe to the configuration of the complex
> defined in a different universe? If so, what aletrnative do you  
> recommend?
> A speedy reply would be great!

You risk running into a problem when adding a displacement (a  
ParticleVector object) from one universe to the configuration of  
another universe. In fact, this shoud fail with an error message. The  
reason is that nothing guarantees that the internal atom order is the  
same, or even that the universe contain corresponding atoms. It's not  
the different force fields that cause the problem, but the existence  
of two separate universes.

My suggestion is to use a single universe and two configurations: one  
for the complex, and one for the unbound form. In the latter you  
would simply move the two elements so far apart that there is no  
interaction, i.e. beyond the largest cutoff in your system. Depending  
on what calculation you want to do, you change the force field of  
your universe (universe.setForceField(...)).

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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