AMBER: MM-PBSA calcuation for drug dna complex in 2:1 ratio

From: saurabh agrawal <>
Date: Tue, 12 Jun 2007 14:25:09 +0100 (BST)

Dear Amber Users,

I want to calculate binding free energy for dna drug
complex in 2:1 ratio. How do I calculate it.
Does Giving 2 at Ligand option in MM-pbsa script is
correct way for free energy calculation?

because in the mm-pbsa script following line is

"LIGAND - Set to 1 if free energy difference is

I am not understanding how to solve the problem.

Any suggestion will be of great importance for me.



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Received on Wed Jun 13 2007 - 06:07:31 PDT
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