AMBER: MM_PBSA with complex plus Ion

From: <saccenti.cerm.unifi.it>
Date: Fri, 21 Sep 2007 16:26:58 +0200 (CEST)

I have a question about how to treat a complex with a metal ion.
That is a I have a complex of the form
A-i-B where A and B are protein and i a metal ion that is bonded to both A
and B.
I would like to extimate the stability and binding energy following the
tutorial exemples that is indeed very clear.

As I need prm top files for Ligand and receptor how to treat the ion?

Many thnks for any clue!

Edo

-- 
Dr Edoardo Saccenti
CERM Magnetic Resonance Center
University of Florence
Fiorgen Foundation
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino
(FI) Italy
Tel: +39 055 4574281
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Received on Sun Sep 23 2007 - 06:07:42 PDT