AMBER Archive (2007)

Subject: AMBER: Essential ions and water molecules in MMPBSA computations

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Mar 12 2007 - 03:13:56 CST

Dear Amber community,

I have such a complex system that one Na+ ion and two water molecules make a significant contribution to the stability of the complex and I personally wouldn't want to remove them during MMPBSA computations. I was wondering if any has succeeded including such essential ions and water molecules in MMPBSA computations. Can anyone please guide me on how this can be done and what outcome can be expected by MMPBSA for a complex system including ions and water molecules?

My best regards,

Jenk

 
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