special belly minimization

From: Didier Rognan <didier.rognan_at_aspirine.u-strasbg.fr>
Date: Wed 25 Apr 2001 12:40:51 +0200

Dear AMBER users

Has anyone already found a trick to suppress force evaluation on a belly
group during an AMBER minimization/dynamics?

What I would like to do is a multi-ligand directed energy refinement of a
protein active site as following:
1. fitting all ligands (say 10) according to known pharmacophoric patterns
and putting these 10 ligands in a belly group
2. minimizing the protein with the 10 ligands docked in the binding site
(according to expl. data)

Step 2 implies that the intermolecular interactions between molecules
defining the belly group are not calculated. One way of doing it would be
to supress evaluation of forces on the belly atoms.

Is that possible with the current code ?

Thanks for your answers
Dr. Didier ROGNAN
Laboratoire de Pharmacochimie de la Communication Cellulaire
74, route du Rhin - B.P. 24
F-67401 Illkirch

phone: +33(0)3 90 24 42 35
mobile: +33(0)6 89 56 24 46
fax: +33(0)3 90 24 43 10
email: didier.rognan_at_pharma.u-strasbg.fr
www: http://lead6.u-strasbg.fr/bioinfo
Received on Wed Apr 25 2001 - 03:40:51 PDT
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