Subject: Amber94 force field parameters for Saquinavir, Indinavir

From: Michiel Jan Laurens de Hoon <mdehoon<<at>>ims.u-tokyo.ac.jp>
Date: Fri, 25 Jul 2003 13:27:10 +0900

Hi,

I am using Konrad Hinsen's Molecular Modeling Toolkit to estimate 
changes caused by mutations in the HIV genome in the binding energy 
between the HIV protease and the Indinavir and Saquinavir protease 
inhibitors.  Using Modeller, I can create PDB files with the estimated 
structure of a mutated HIV protease complexed to the protease.  To 
calculate the interaction energy, I would need the Amber94 force field 
parameters for the inhibitor.  Are such parameters available somewhere? 
  I didn't find them on the Amber web site, though I would think that 
Indinavir and Saquinavir are well-studied molecules.  Is it possible to 
mock up the interaction between the protease and the inhibitor? 
Something quick and dirty is fine for what I am doing.

Many thanks in advance,

Michiel de Hoon,
Univsersity of Tokyo.

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon