Force Fields for AutoDock
AutoDock Parameter Files
In AutoDock4, force field interactions are defined in parameter files. Normally the parameter files are internal to AutoDock and AutoGrid, including the optimized parameters described in our publications. Users may modify parameters for special cases by using the “parameter_library” keyword (“parameter_file” also works). The “parameter_library” keyword requires one argument, the name of the parameter file. Several alternative parameter files are available:
- AD4.1_bound.dat
- This is the default parameter file for AutoGrid 4.2 and AutoDock 4.2; the coefficients of this model were derived using the assumption that the unbound ligand has the same conformation as the bound ligand. Please note these two caveats: 1- If the DPF keyword “compute_unbound_extended” is present in the docking parameter file, AutoDock 4.2 will switch from this set of parameters to those in AD4_parameters.dat. 2- If you intend to use the parameters in AD4_parameter.dat, the same parameters should also be used for the AutoGrid 4.2 calculation.
- AD4.1_compact.dat
- The coefficients of this model were derived using the assumption that the unbound ligand is in the compact conformation. This is not currently supported in AutoDock 4.
- AD4.1_extended.dat
- This is the default parameter file for AutoGrid 4.0.0 and AutoDock 4.0.1. It can also be used as an alternative parameter file for AutoGrid 4.2 and AutoDock 4.2, although the AD4.1_bound.dat file is the default for version 4.2. The coefficients of the model were derived using the assumption that the unbound ligand is in the extended conformation. The DPF keyword “compute_unbound_extended” _must_ be used with this set of parameters.
- AD4_parameters.dat
- This is the default parameter file for AutoGrid 4.0.0 and AutoDock 4.0.1; the coefficients of the model were derived using the assumption that the unbound ligand is in the extended conformation. The DPF keyword “compute_unbound_extended” must be used with this set of parameters.
Changing Atom Types and Parameters
- The default force-field parameters for 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?.
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 WaalsΔGvdW = WvdW ∑i, j ( Aij / rij12 – Bij / rij6 )
- Hydrogen BondingΔGH-bond = WH-bond ∑i, j E(t) * ( Cij / rij12 – Dij / rij10 + Ehbond )
- Electrostatics – see Coulomb’s LawΔGelec = 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.
Torsional Free Energy Change on Binding
- TorsionalΔGtor = Wtor Ntor
(where Ntor is the number of all rotatable bonds, excluding guanidinium and amide bonds etc.)
Complete equation:
AutoDockZN forcefield | AutoDock
This section provides code, documentation and examples to perform docking simulations
with the AutoDock4Zn forcefield described in the paper:
AutoDockZN tutorial (83 kBytes) 
AutoDockZN files (266 kBytes)