ADL: degree of freedom and no. of torsion

Tee Pioj tee_piorj at yahoo.com
Tue Jan 1 00:26:14 PST 2008


Hello, Dockers
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!!
 
Best regards,
Teerapong Pirojsirikul


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