AMBER Archive (2009)

Subject: [AMBER] MM-PBSA with explicit water

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Fri May 15 2009 - 01:45:23 CDT

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

===========================================================================

      Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber