ADL: Calculation of the free energy of binding using epdb or AutoDock4.1Score

annalisa bordogna annalisa.bordogna at gmail.com
Mon Apr 6 05:48:36 PDT 2009


Hi everybody!

I tried to calculate the Free Energy of Binding on a pose generated by
AutoDock using both the command epdb and AutoDock4.1Score and I found that
the results were different for the three cases:
*
1) epdb:*
Estimated Free Energy of Binding    =   -8.42 kcal/mol  [=(1)+(2)+(3)-(4)]
epdb: USER    (1) Final Intermolecular Energy     =  -20.50 kcal/mol
epdb: USER        vdW + Hbond + desolv Energy     =  -19.52 kcal/mol
epdb: USER        Electrostatic Energy            =   -0.98 kcal/mol
epdb: USER    (2) Final Total Internal Energy     =   +0.00 kcal/mol
epdb: USER    (3) Torsional Free Energy           =  +12.07 kcal/mol
epdb: USER    (4) Unbound System's Energy         =   +0.00 kcal/mol
*
2) AutoDock4.1Score:*
   AutoDock4.1Score     estat      hb            vdw      dsolv    tors
       -9.2842             -0.9357 -4.0624 -24.7674  7.3561  13.1252

*3) energy calculated during docking:*
DOCKED: USER    Estimated Free Energy of Binding    =  -14.60 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER    (1) Final Intermolecular Energy     =  -23.84 kcal/mol
DOCKED: USER        vdW + Hbond + desolv Energy     =  -22.94 kcal/mol
DOCKED: USER        Electrostatic Energy            =   -0.90 kcal/mol
DOCKED: USER    (2) Final Total Internal Energy     =   -1.72 kcal/mol
DOCKED: USER    (3) Torsional Free Energy           =   +9.88 kcal/mol
DOCKED: USER    (4) Unbound System's Energy         =   -1.08 kcal/mol

Does anybody know why?
Now, I don't know which of the three methods is reliable for such a
calculation!

Thank you very much for your help.
Best regards,
Annalisa

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Annalisa Bordogna
PhD. Student
DISAT - Università degli Studi di Milano Bicocca
Milano - Italy
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