[MMTK] NMA

vanitha@cs.wisc.edu vanitha at cs.wisc.edu
Fri Mar 17 14:57:26 CET 2006


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

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.
Do you think you'd be able to re-write your procedure keeping this in mind?
Sorry to bother you!

Thanks,

- Vanitha


> On Mar 17, 2006, at 13:59, vanitha at cs.wisc.edu wrote:
>
>> 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
>> array.
>> 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.
>
> No, that won't work. As soon as you add or remove molecules, the
> universe becomes for all practical purposes a different one. This
> means that for example the  normal modes computed in your step 3
> won't be compatible with the universe after step 4.
>
> Here is my suggestion:
>
> 1) Put the complex into the universe.
> 2) Make a copy of the configuration:
> 		complex_configuration = copy(universe.configuration())
> 3) Move one of the ligands away:
> 		ligand1.translateBy(Vector(10., 0., 0.))
>     10 nm is sufficient for a deformation force field, but feel free
> to use more.
> 4) Add the deformation force field:
> 		universe.setForceField(DeformationForceField(cutoff=2.5))
> 5) Calculate the normal modes:
> 		modes = EnergeticModes(universe)
> 6) Restore the complex configuration:
> 		universe.setConfiguration(complex_configuration)
> 7) Set the Amber force field:
> 		universe.setForceField(Amber99ForceField(...))
> 8) Do refinement using the normal mode vectors.
>
> A comment on the normal modes (step 5): Since the two molecules do
> not interact, you will have a total of 12 zero-energy modes (the
> translation and rotation of the two molecules). Any other mode will
> contain a deformation of only one of the two molecules, except if the
> two molecules are identical (in that case there are degenerate
> modes). So even though you calculate the modes for the two molecules
> together, you can still separate them into deformations of the
> individual molecules, which I think is what you want.
>
> 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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