Subject: Internal Ligand Energy in Autodock

From: Robert Flight <[email-masked]>
Date: Sat, 7 Dec 2002 15:43:03 -0400

Hi All,

I am trying to determine how Autodock calculates the internal energies of the 
docked poses generated from a docking run.  There is plenty of documentation 
on how the intermolecular energies are calculated (main references from the 
Autodock site) but I was not able to find anything in the literature on how 
Autodock calculates the internal energies except for a brief mention that it 
happens (J. Comp. Chem. 1998 and J. Mol. Rec. 1996).

> From what I can understand, pairwise interactions between all the ligand atoms 
are calculated and summed for internal energy, vs the interactions between the 
ligand and receptor atoms for intermolecular energy.  Is this right?  And does 
the calculation take into account any out of plane distortions and non-ideal 
bond angles and distances?

Any information on this subject would be appreciated, or even a reference that 
I could look at.  Responses will be summarized and posted.

Thank you very much for your help,

Robert

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Robert Flight
Masters Student
Department of Chemistry
University of New Brunswick
Fredericton, NB  Canada  E3B 6E2
e-mail: [email-masked]
 
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