Subject: Re: CCL:Normal Modes for large proteins

From: Konrad Hinsen <[email-masked]>
Date: Wed, 27 Feb 2002 14:41:14 +0100

Ben Carrington <[email-masked]> writes:

> Can anyone suggest how I go about performing normal modes calculations
> on large systems - protein complexes to be exact. At the moment I cannot
> get any programs to run due to the large amount of memory needed. Can I
> split this calculation up?

There are various techniques to calculate normal modes for large
systems, approximately and/or iteratively. It all depends on what you
need the normal modes for. If you are interested in low-frequency
modes for large systems, I can propose a method described in

    K. Hinsen
    Analysis of domain motions by approximate normal mode calculations
    Proteins 33(3), 417-429 (1998)

and implemented in the Molecular Modelling Toolkit:

    http://dirac.cnrs-orleans.fr/MMTK/

as well as in an interactive domain motion analysis tool:

    http://dirac.cnrs-orleans.fr/DomainFinder/

For some applications, see

    K. Hinsen, A. Thomas, M.J. Field
    Analysis of domain motions in large proteins,
    Proteins 34(3), 369-382 (1999)

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