[MMTK] [Fwd: Re: NMA]

vanitha@cs.wisc.edu vanitha at cs.wisc.edu
Fri Mar 17 03:28:33 CET 2006

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!


- Vanitha

> On 10.03.2006, at 13:58, vanitha at cs.wisc.edu wrote:
>> I see that one can do a sparse matrix normal mode analysis within
>> MMTK. Is
>> the Implicitly Restarted Arnoldi method (ARPACK) being used to
>> compute the
>> normal modes in this case. Also, what model does the NMA code in
>> MMTK use?
>> Elastic Network Model or a Force-field based one?
> An Elastic Network Model is nothing else but a particular choice of
> force field. MMTK contains two Elastic Network force fields
> (DeformationForceField and CalphaForceField) and one all-atom force
> field (Amber94ForceField), which can all be used for normal mode
> analysis.
> As for the use of sparse matrices, note that you need to install the
> add-on module MMTK_SparseModes, which contains ARPACK code plus an
> interface module. The reason for keeping this separate is that the
> ARPACK licensing conditions are not clear to me. I prefer to stay
> away from legal trouble.
> Without this add-on module, you can still use sparse matrices in
> combination with an explicit basis. In that case, the Hessian for the
> given basis is calculated from a sparse all-atom Hessian, and
> diagonalized as usual. If the basis is much smaller than the all-atom
> basis, and the force field has a small effective cutoff, this uses
> much less memory than the standard approach.
> Konrad.
> --
> ------------------------------------------------------------------------
> -------
> Konrad Hinsen
> Laboratoire Leon Brillouin (CEA-CNRS), 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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