ADL: docking energy difference between autodock3 and autodock4

lanyy at sjtu.edu.cn lanyy at sjtu.edu.cn
Sun Oct 28 19:24:14 PDT 2007


I used the same parameters to do autodock3 and autodock4, but the result energies different greatly. Can anybody tell me the reason. Thanks!

	LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER
	___________________________________________________

Keeping original residue number (specified in the input PDBQ file) for outputting.

MODEL       49
USER    Run = 49
USER    Cluster Rank = 1
USER    Number of conformations in this cluster = 10
USER  USER    RMSD from reference structure       = 69.334 A
USER  USER    Estimated Free Energy of Binding    =   -4.96 kcal/mol  [=(1)+(3)]
USER    Estimated Inhibition Constant, Ki   =   +2.31e-04       [Temperature = 298.15 K]
USER    USER    Final Docked Energy                 =  -16.64 kcal/mol  [=(1)+(2)]
USER    USER    (1) Final Intermolecular Energy     =  -14.61 kcal/mol
USER    (2) Final Internal Energy of Ligand =   -2.03 kcal/mol
USER    (3) Torsional Free Energy           =   +9.65 kcal/mol




	LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER
	___________________________________________________


Keeping original residue number (specified in the input PDBQ file) for outputting.

MODEL        8
USER    Run = 8
USER    Cluster Rank = 1
USER    Number of conformations in this cluster = 1
USER  USER    RMSD from reference structure       = 72.224 A
USER  USER    Estimated Free Energy of Binding    =   -8.50 kcal/mol  [=(1)+(2)+(3)-(4)]
USER    Estimated Inhibition Constant, Ki   =  586.25 nM (nanomolar)  [Temperature = 298.15 K]
USER    USER    (1) Final Intermolecular Energy     =   -8.74 kcal/mol
USER        vdW + Hbond + desolv Energy     =   -5.05 kcal/mol
USER        Electrostatic Energy            =   -3.69 kcal/mol
USER    (2) Final Total Internal Energy     =   -1.66 kcal/mol
USER    (3) Torsional Free Energy           =   +0.00 kcal/mol
USER    (4) Unbound System's Energy         =   -1.89 kcal/mol



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