An Amber question

From: Fabio Schoen <>
Date: Thu 15 Nov 2001 09:11:06 +0100

Dear Sirs,
We would like to ask you whether it is possible/easy with the Amber package to obtain the coefficients in the force field.
I explain myself: what we would like to have is a system which reads a PDB file (with no modifications of any kind), interprets its contents and generates a file containig atom charges, VdW coefficients, etc, i.e. all of the numeric data which is used in defining the amber force field.

The reason we are asking this is that we are mathematicians and engineers (not chemists or biologists) and we are testing some global optimization codes for (rigid) protein docking. We are looking for test examples and we would like to use the Amber FF as it became more or less a standard. But we are not going to use Amber itself, as, first of all, we code in C++ and have difficulties in mixing with fortran and/or f2c generated code, and also because we need an extremely efficient code, so that we cannot afford to have the overhead of such a general system as Amber is.

So we coded the FF (and the gradients), and we just need the numeric coefficients.
Our colleagues in chemistry here in Florence do possess an amber license, so if you tell us that this is easy, we can immediately test your suggestions.
Thank you and best regards,
fabio schoen

Fabio Schoen Professor of Operations Research
tel: +39 0554796.358 fax: +39 0554796.363
Dip. Sistemi e Informatica Univ. di Firenze - via di S.Marta 3, 50139 FIRENZE (Italy)
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Received on Thu Nov 15 2001 - 00:11:06 PST
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