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 = WvdW ∑i, j ( Aij / rij12 - Bij / rij6 )
- Hydrogen Bonding
ΔGH-bond = WH-bond ∑i, j E(t) * ( Cij / rij12 - Dij / rij10 + Ehbond )
- Electrostatics - see Coulomb's Law
ΔGelec = Welec ∑i, j ( qi * qj ) / ( ε(rij) * rij )
- Desolvation (AutoDock 3)
ΔGdesolv = Wdesolv ∑i (C), j (Si * Vj * exp ( -rij2 / (2 * σ2) ) )
- see also AutoDock 4 Desolvation Free Energy for more details about the AutoDock 4 desolvation term.
Estimated Change in Torsional Free Energy when the Ligand goes from Unbound to Bound
ΔGtor = Wtor Ntor
(where Ntor is the number of all rotatable bonds, excluding guanidinium and amide bonds etc.)
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?.