Subject: Force Fields & Torsion Parameters

From: Catherine Cresson <ccresson!at!Princeton.EDU>
Date: Mon, 29 Sep 2003 12:47:07 -0400 (EDT)

Dear CCLers,

  I am working on a docking algorithm with a novel binding site
representation.  However, I do not wish to re-invent an intramolecular
forcefield for the peptides I am docking into my protein.  I am very
familiar with InsightII, which unfortunately does not allow me to use my
binding site model with their forcefields.  Does anyone have any
suggestions of free (or purchasable) software that might be more
compatible with my needs?
  Also, to circumvent this problem,  I tired to create a simple forcefield
with minimal atom types and only terms for bond stretching, angle bending,
torsion, and nonbonded interactions.  The difficult portion of this task
is finding the correct parameters for the torsion term.  I've searched the
literature and I seem to find either functional representations or
rotamers libraries, but I am unsure exactly how to combine these two
aspects to actually implement a working code.  Can you give me any
guidance and advice?
  Thanks so much for reading through my questions and I look forward to
reading your responses.

Catherine Cresson

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Catherine Cresson
Department of Chemistry
Princeton University
Princeton, NJ 08544
lab: (609)258-2707
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