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Adding new atom parameters to AutoDock

This How-to applies to: Any version.
This How-to is intended for: Any audience.

To use AutoDock with molecules that have atoms of types not included in the AutoDock force field calibration such as heavy metal ions, estimate values of Rii, epsii, vol and solpar parameters for each new type, create a modified atomic parameter file which includes a line for each of the new types and add 'parameter_file <modified_parameter_filename>' to the *.gpf for AutoGrid and the *.dpf for AutoDock.

Many atom types, such as heavy metal ions, were not included in the force field calibration because experimental data was not available for complexes that include these atoms. If you need to use these atom types in your application, you will need to estimate 4 atomic parameters for each atom type to be added. You will need to create a modified atomic parameter file containing the new types.  Finally, you will need to direct AutoGrid and AutoDock to use the modified atomic parameter file instead of the default values included internally in the programs.

The default atomic parameter file, AD4.1_bound.dat, is available online here:

For metal ions, an example entry in the parameter file is:
atom_par Zn     1.48  0.550   1.7000  -0.00110  0.0  0.0  0  -1  -1  4

The first four numbers are the ones to change:
Rii = sum of vdW radii of two like atoms (in Angstrom)
epsii = vdW well depth (in Kcal/mol)
vol = atomic solvation volume (in Angstrom^3)  (4/3*pi*(Rii/2)**3)
solpar = atomic solvation parameter

Then, in the parameter files for AutoGrid and AutoDock (*.gpf and *.dpf files), add this command at the top of the file:
parameter_file <modified parameter file name>

A full description of these files is included in the AutoDock4.2 User Guide, available at the AutoDock site:

by Ruth Huey last modified 2011-07-06 10:00
Contributors: Sargis Dallakyan

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