AMBER Archive (2007)

Subject: AMBER: MM_PBSA with complex plus Ion

From: saccenti_at_cerm.unifi.it
Date: Fri Sep 21 2007 - 09:26:58 CDT

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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