AMBER Archive (2007)

Subject: AMBER: MMPBSA with water molecule in active site

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Sun Mar 18 2007 - 11:25:44 CST

Dear Amber users,

I want to do mmpbsa calculation for dna drug
interaction in the presence of one water molecule and
K+ ion at the active site.
Is it possible to calculate binding free energy in the
presence water and ions with mmpbsa or any other
method?

Thanking you in advance.

saurabh

                
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