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Equations

by morris last modified 2009-07-16 12:37

Here is a summary of the equations used in the AutoDock force field.

Free Energy Coefficients

The molecular mechanics-based and empirical terms are multiplied by coefficients that are determined by linear regression analysis of complexes with known 3D-structures and known binding free energies. In the equations on this page, these weights are WvdW, WH-bond, Welec, Wdesolv and Wtor. In AutoDock 4, these free energy weights, FE_coeff_vdW, FE_coeff_hbond, FE_coeff_estat, FE_coeff_desolv and FE_coeff_tors, can be set in the parameter file.

Molecular Mechanics Terms

  • van der Waals

    ΔGvdW = WvdWi, j ( Aij / rij12 - Bij / rij6 )

  • Hydrogen Bonding

    ΔGH-bond = WH-bondi, j E(t) * ( Cij / rij12 - Dij / rij10 + Ehbond )

  • Electrostatics - see Coulomb's Law

    ΔGelec = Weleci, j ( qi * qj ) / ( ε(rij) * rij )

  • Desolvation (AutoDock 3)

    ΔGdesolv = Wdesolvi (C), j (Si * Vj * exp ( -rij2 / (2 * σ2) ) )

Estimated Change in Torsional Free Energy when the Ligand goes from Unbound to Bound

  • Torsional

    ΔGtor = Wtor Ntor
    (where Ntor is the number of all rotatable bonds, excluding guanidinium and amide bonds etc.)

Complete equation:



Changing Atom Types and Parameters

Note that in AutoDock 4, there are more atom types allowed for the molecules, and these are specified in PDBQT-formatted files.

The default force-field parameters for these atom types can be overrided using the "parameter_file" command in the GPF and DPF. This command requires one argument, namely the filename of the ".dat" file that contains the linear free energy model's coefficients and the atom parameters; the default values can be found in "AD4_parameters.dat" which resides in the source code distribution. For more details, read the FAQs, Where do I set the AutoDock 4 force field parameters? and How do I add new atom types to AutoDock 4?.


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