[AMBER] Query regarding considering water molecules

From: sonam bhatia <sonamniper.bhatia.gmail.com>
Date: Wed, 6 Apr 2011 21:16:02 +0530

I want to perform MD simulation on the protein containing Mg and Zn ions and
5 water molecules in active site which are necessary to kept during
simulation. I am facing problem how to consider those water molecules,
either part of protein or as a part of ligand?
 Or any other method is there for their treatment? 


-- 
*Sonam Bhatia,*
*Ph.D. Scholar,
Department of Medicinal chemistry,
National Institute of Pharmaceutical Education and Research (NIPER),
Sector 67, phase 10,S.A.S Nagar,
Punjab-160062. India*
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Received on Wed Apr 06 2011 - 09:00:02 PDT
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