AMBER Archive (2009)

Subject: [AMBER] Fw: MM-PBSA with explicit water

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Fri May 15 2009 - 01:43:46 CDT

/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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--- On Fri, 15/5/09, mathew k varghese <mathew_kvarghese_at_yahoo.co.in> wrote:

From: mathew k varghese <mathew_kvarghese_at_yahoo.co.in>
Subject: MM-PBSA with explicit water
To: "amber mail list amber" <amber_at_scripps.edu>
Date: Friday, 15 May, 2009, 12:12 PM

Hello,

I want to do some MM-PBSA calculations of some nucleic acid ligand systems. How can I keep some water molecules near the binding site in the calculations. Should I treat the water as part of ligand?

Thanks in advance

/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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