vanitha@cs.wisc.edu vanitha at cs.wisc.edu
Fri Mar 17 13:59:19 CET 2006

Can I try the following approach:-

1) Create Universe with Deformation Force field
2) Add unbound structure 1.
3) Compute the normal mode for it and store the normal mode vectors in an
4) Remove unbound structure 1.
5) Add unbound structure 2 and repeat steps 3 & 4 for structure 2.
6) Set Force field to the all-atom Amber94ForceField.
7) Add the complex containing structure 1 and 2.
8) Perform refinements using the normal mode vectors stored in the arrays.

Does this make sense? I'm not sure how to go about doing what you
suggested and that's why I'm looking at this approach.


- Vanitha

> Thanks. Would it be possible for you to give me an example of how to set
> up two configurations and move the two unbound structures apart so that
> they don't interact? It will be great even if you can point me to some
> examples within MMTK where this is being done.
> Also, can you conceptually explain what the universe is all about? In
> addition to the objects I am adding, does it contain a solvent, etc?
> Thanks again,
> - Vanitha
>> 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.
>> --
>> ---------------------------------------------------------------------
>> 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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