Subject: Autodock: Ligand energy

From: David Smith <[email-masked]>
Date: Thu, 16 May 2002 18:14:04 -0400

Hello Autodockers,

I have a simple question for you this time regarding the energy of the
ligand alone after docking.

The results I get are:

USER    Final Docked Energy                 =  -10.51 kcal/mol 
[=(1)+(2)]
USER    
USER    (1) Final Intermolecular Energy     =  -10.13 kcal/mol
USER    (2) Final Internal Energy of Ligand =   -0.38 kcal/mol
USER    (3) Torsional Free Energy           =   +3.74 kcal/mol

My Question is:

Does the "Final Internal Energy of Ligand" represent the energy of the
ligands particular conformation alone, apart from any outside energies
such as from the macromolecule?

In other words If I want to compare the energy of one docked ligand to
the energy of another is this the calculations I could use to do that.

thanks,

Dave