Subject: determine Amber ff coefficients for pdb file

From: Addis <[email-masked]>
Date: Wed, 19 Dec 2001 18:52:13 +0100

We started to work on biomolecular docking by means of optimization algorithms. 
We take a configuration from the pdb database, with two molecules, we split the 
complex and try to recostruct the docking minimizing the potential energy. We 
have been using a ff ( Gromos), but the problem is that in our fragment database 
  there aren't all we need and we aren't able to introduce new ones, in fact our 
knowledge in computational chemistry is very little.
We would like to use Amber (in fact it is on of the most frequently used), so 
it's easy to make comparison between published and our results. The problem in 
using Amber is that we don't simply need  the value of the ff for a certain 
configuration, but we need all the parameters involved for evaluating the 
potential by ourself: in fact in our algorithm we need to evaluate the ff 
function many times, and in some cases we consider modification of this function.
Another problem is finding input data for the algorithm: we would like to use 
the pdb archive, but some time we find proteins in which there are fragment 
different from aminoacids.
So we would to know whether it is possible to costruct rules for determine from 
a file in pdb format (or a large part of these) the coefficient needed for 
evaluate the Amber ff ( for example Van der Walls coefficients or dihedral 
angles and coefficients).

Thank you very much,

     Addis Bernardetta

     [email-masked]