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How do I add new atom types to AutoDock 4?

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This FAQ applies to: AutoDock 4

AutoDock version 4.0 has parameters for H, C, N, O, F, Mg, P, S, Cl, Ca, Mn, Fe, Zn, Br and I. What do you do if your molecule has an atom type that isn't already parameterised?

The various parameters in the AutoDock 4 scoring function are described in another FAQ, Where do I set the AutoDock 4 force field parameters?. The atom types' names and parameters are specified in a file that can be called anything, but by default is called "AD4_parameters.dat". You can find a copy of this default file in the source code of AutoGrid and AutoDock. This parameter file can be specified by the "parameter_file" keyword in the GPF and DPF, but if this keyword is not given, then AutoGrid and AutoDock use the default values. So the only time you need to use the "parameter_file" keyword is when you want to change the default values, or to add new atom types.

How do I add new atom types?

Important: Bear in mind that the AutoDock 4 scoring function was calibrated for the current set of atom types, and that if you add new ones, strictly speaking you should perform a re-calibration of the force field to determine the correct coefficients for the molecular mechanics terms and the empirical term of the linear free energy model.

You will need to find, compute or set the following values for each new atom type, which you specify after the "atom_par" keyword. Note that the values on each "atom_par" line are space delimited, not fixed width. You will need to add one "atom_par" line for every new atom type. It is possible to define 'synonyms' for atom types, by repeating the numerical atom parameter lines for every variant of the atom type's one- or two-character name.

  • name of the atom type; this can be one or two characters long, and should correspond to the atom type at the end of ATOM or HETATM lines in PDBQT files; specify this in the "Atom Type" field
  • van der Waals radius of the atom/ion (in Angstrom); specify twice this value in the "Rii" field
  • epsilon or energy well depth for two like interacting atoms/ions (in Kcal/mol); specify in the "epsii" field
  • volume of the atom/ion (in Angstrom^3); compute this from 4/3 * PI * (Rii/2)^3; specify in the "vol" field
  • atomic solvation parameter of the atom/ion; the ai or "ASP" values in the equation for Si in the description of the Desolvation Free Energy Term in AutoDock 4; specify this in the "solpar" field
  • hydrogen bonding radius (in Angstrom); for non-hydrogen-bonding atom types this is 0.0; specify this in the "Rij_hb" field
  • hydrogen bonding energy well depth (in Kcal/mol); for non-hydrogen-bonding atom types this is 0.0; specify this in the "epsij_hb" field
  • hydrogen bonding type; an integer; for non-hydrogen-bonding atom types this is 0; specify this in the "hbond" field
  • receptor type index; an integer; default value is -1; specify this in the "rec_index" field
  • grid map index; an integer; default value is -1; specify this in the "map_index" field
  • bond type index; an integer; default value is 4; specify this in the "bond_index" field

The last six values (0.0 0.0 0 -1 -1 4) will be the same if the atom type is not involved in hydrogen bonding.

Note that a comment can be specified after a number sign symbol, #

Remember to use the "parameter_file AD4_parameters.dat" command in both the GPF and DPF, so that the new parameters are used in both the AutoGrid pre-calculation of the grid maps, and in the AutoDock dockings. Specify this command on the first line of the GPF and DPF files.

by morris last modified 2007-07-26 18:31

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