AMBER Archive (2007)

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

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Tue Jun 12 2007 - 08:25:09 CDT

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
written.

"LIGAND - Set to 1 if free energy difference is
calculated."

I am not understanding how to solve the problem.

Any suggestion will be of great importance for me.

saurabh

 

                
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