ADL: docking energy difference between autodock3 and autodock4

Daniel Jana dfjana at gmail.com
Mon Oct 29 03:30:29 PDT 2007


Hello!

According to an email sent by Anurag in the 16th of October:

"With reference to your queries on the Autodock archieves, the main
difference between autodocks' versions 3 and 4 is that 3 takes into account
only the ligand flexibility where as version 4 also considers the side-chain
flexibility of the receptor molecule."

Hope this helps!

Daniel

On 29/10/2007, lanyy at sjtu.edu.cn <lanyy at sjtu.edu.cn> wrote:
> 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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>


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