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Date: Fri, 27 Sep 2002 10:50:05 -0400
From: Richard Gillilan <reg8 _-at-_)cornell.edu>
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To: olivier walker <oliwalk: at :wam.umd.edu>
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Subject: Re: CCL:useful software for dual domain protein conformational search?
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This sounds like a good candidate for rigid-body
mechanics. You could treat the two domains as rigid
but NOT fixed in space. You could also apply additional
constraints to the bond lengths if you wanted to increase the
efficiency of the dynamics run. I believe the MBO(N)D program
available from (Accelrys?) can do this sort of thing.
There were a couple papers in J. Comp. Chem. on combining 
quaternion-based mechanics with SHAKE-type constraints
a few years ago:

    Forester TR, Smith W
    SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies
    J COMPUT CHEM 19 (1): 102-111 JAN 15 1998)

    Wu XW, Sung SS
    Constraint dynamics algorithm for simulation of semiflexible macromolecules
    J COMPUT CHEM 19 (14): 1555-1566 NOV 15 1998 


Richard Gillilan
MacCHESS, Cornell


olivier walker wrote:
> 
> Hi all,
> 
> I'm currently studying a dual domain protein. I would like to generate all
> possible conformations including some restraints.
> Basically, I want to study all possible conformation of the link between
> the two domains (8 residues) and freeze the two domains (not totally
> because I would like to follow the shift of the domains with the
> conformation change of the link).
> 
> My questions are:
> 
> * what method should I consider (MD, monte carlo, annealing.....)?
> * The most important: what is the best suitable software for this kind of
> study ?
> * using this software, is it possible to monitor energy, distances between
> given residues and other features?
> 
> Thanks in advance for your help
> 
> olivier.