[gmx-users] RE: Docking Energy confirmation

[Spiwok Vojtech]

> I'm doing docking "calculations" with Autodock3.05.
> My question is, is there any way to use the energy minimization procedure
> from
> Gromacs to relax the conformations obtained from autodock and have a
> better estimate
> of their energy (in comparision tothe energy that autodock gives as
> result)?
>
If you prefer accuracy over throughput then Prodrug/gromacs minimization
and dynamics could be a choice. Autodock uses its scoring function
which includes force-field terms and empiricaly derived terms for solvent
effect and conformational entropy of ligand. Therefore only force-field
energy itself (either from gromacs or autodock) can hardly be a better
for scoring of ligands. You might try free energy calculation by linear
interaction energy (g_lie of gromacs).

http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/gmx.pdf
http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf

Vojtech Spiwok
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