ADL: docking energy difference between autodock3 and autodock4

mswingle at jaguar1.usouthal.edu mswingle at jaguar1.usouthal.edu
Mon Oct 29 20:05:55 PDT 2007


Hi,

It looks like you did a flexible docking with autodock3 and a rigid docking with autodock4 (OR you set free 
energy per torsional DOF to zero).

> USER    (3) Torsional Free Energy           =   +9.65 kcal/mol


> USER    (3) Torsional Free Energy           =   +0.00 kcal/mol


----- Original Message -----
From: lanyy at sjtu.edu.cn
Date: Sunday, October 28, 2007 9:34 pm
Subject: ADL: docking energy difference between autodock3 and autodock4
To: autodock <autodock at scripps.edu>


> 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
> 
> ________________________________________________
> --- ADL: AutoDock List  ---  ---


More information about the autodock mailing list