ADL: Autodock 4 energy break-down

Dong Xu dxu at mccammon.ucsd.edu
Wed Nov 7 12:59:06 PST 2007


Hi,

I wanted to second Arneh's question. How do we get a energy break-down of the
vdW + Hbond + desolv Energy ?

If a source code modification is needed, can anyone tell us where to look for?

Thanks,
Dong Xu

---------- Forwarded message ----------
From: Arneh Babakhani <ababakha at mccammon.ucsd.edu>
Date: Nov 7, 2007 8:37 AM
Subject: ADL: Extracting the Desolvation Energy from a dlg file
To: autodock at scripps.edu


Hello,

How does one extract the desolvation energy from a particular cluster, in
a dlg file?

For instance, in the excerpt below, we can see that the desolv Energy is
encompassed in the Final Intermolecular Energy (vdW + HBond + desolv
Energy = -6.50 ).   But how do we determine the values of each of the
three (or at least two) of the terms on the left hand side, for this
particular cluster?

Thanks,

USER    Cluster Rank = 5
USER    Number of conformations in this cluster = 14
USER
USER    RMSD from reference structure       = 51.638 A
USER
USER    Estimated Free Energy of Binding    =   -6.73 kcal/mol
[=(1)+(2)+(3)-(4)]
USER    Estimated Inhibition Constant, Ki   =   11.67 uM (micromolar)
[Temperature = 298.15 K]
USER
USER    (1) Final Intermolecular Energy     =   -6.50 kcal/mol
USER        vdW + Hbond + desolv Energy     =   -6.40 kcal/mol
USER        Electrostatic Energy            =   -0.11 kcal/mol
USER    (2) Final Total Internal Energy     =   +6.40 kcal/mol
USER    (3) Torsional Free Energy           =   +0.82 kcal/mol
USER    (4) Unbound System's Energy         =   +7.45 kcal/mol

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