ADL: Internal Energy and Unbound System's Energy

rob yang nextgame at
Wed Mar 5 09:17:32 PST 2008

Hi list,
I am wondering how autodock4 calculates the "Final Total internal Energy" and the "Unbound System's Energy". I understand that this is a major part of the improvement over autodock3. 
The reason why I am asking is that when I tried to re-score (using epdb option) a docking pose, I get the same intermolecular energy (which is good), but different Internal energy and unbound energy, which leads to different binding energy. I appreciate any pointers and help. Thank you.


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