ADL: (no subject)
tee_piorj at yahoo.com
Tue Jan 1 00:25:02 PST 2008
I'm a forth year student doing my project with autodock3.0.5. I have a paper which is "A Study on Docking Mode of HIV Protease and
Their Inhibitors" saying about dG autodock. I wonder for two things. The first is in the paper say that dG binding(autodock) is come from
Total AutoDock3.0 Gibbs free energy = torsional entropy + lowest AutoDock3.0 energy - internal energy of inhibitor
but the result in dlg file show that estimate binding free energy is from, for example,
Estimated Free Energy of Binding = -13.76 kcal/mol [=(1)+(3)]
Estimated Inhibition Constant, Ki = +8.23e-11 [Temperature = 298.15 K]
Final Docked Energy = -20.44 kcal/mol [=(1)+(2)]
(1) Final Intermolecular Energy = -18.74 kcal/mol
(2) Final Internal Energy of Ligand = -1.70 kcal/mol
(3) Torsional Free Energy = +4.98 kcal/mol
which one is correct ? or which value I should choose?
The second is that I wonder if "no. of torsion" and "torsion degree of freedom" are always the same. How can I determine torsion degree of freedom or what is its concept? I think that these two value aren't the same. The paper says that torsional entropy is from no. of torsion multiplied with coefficient(0.3113) but I found that it's from torsion degree of freedom multiplied with the coefficient instead.
I'm looking for your replies. HAPPY NEW YEAR 2008!!
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