Binding Free Energy

From: Shirley Hui (shirleyh_at_gmail.com)
Date: Thu Feb 01 2007 - 15:40:27 CST

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Hello,

I have a few different DNA structures (11 base pairs) that I would
like to calculate the binding energy of each bound to a protein (to
form a protein-DNA complex).
How do I do this? I have been searching the NAMD mailing list and
Google however I think I am getting more confused as I go.
Do I need to perform an alchemical free energy perturbation?
Has anyone done this before? Any pointers would be appreciated.
Thanks
shirley

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