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Where do I set the AutoDock 4 force field parameters?

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This FAQ applies to: AutoDock 4

Where can I see or change the values of the van der Waals parameters, hydrogen bonding parameters, and/or atomic solvation parameters ? Where can I see which AutoDock 4 atom types are supported, and what parameters they correspond to? Where can see or modify the values of the linear regression coefficients for the linear free energy model?

In AutoDock 4, we have introduced a new command "parameter_file" that takes a new parameter library file that contains the various force field parameters.  In most cases, you will not need to modify these values, but it is important to know where they are and how to change them if necessary.

The standard AutoDock 4 parameters are in the file "AD4_parameters.dat" which can be found in the "autodocksuite-4.n.m/src/autodock-4.x.y" directory of the AutoDock 4 distribution, where n and m are the major and minor version numbers of the AutoDock Suite, and x and y are the major and minor version numbers of AutoDock.  Here is an example:

# $Id: AD4_parameters.dat,v 1.14 2007/04/27 06:01:47 garrett Exp $
# 
# AutoDock 
# 
# Copyright (C) 1989-2007,  Garrett M. Morris, David S. Goodsell, Ruth Huey, Arthur J. Olson, 
# All Rights Reserved.
# 
# AutoDock is a Trade Mark of The Scripps Research Institute.
# 
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

# AutoDock Linear Free Energy Model Coefficients and Energetic Parameters
#                        Version 1.0
#                     $Revision: 1.14 $

# AutoDock 4 free energy coefficients with respect to original (AD2) energetic parameters
#
#               Free Energy Coefficient
#               ------
FE_coeff_vdW    0.1560
FE_coeff_hbond  0.0974
FE_coeff_estat  0.1465
FE_coeff_desolv 0.1159
FE_coeff_tors   0.2744

# AutoDock 4 Energy Parameters

# - Atomic solvation volumes and parameters
# - Unweighted vdW and Unweighted H-bond Well Depths
#
# - Atom Types
# - 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)
# - solpar = atomic solvation parameter
# - Rij_hb = H-bond radius of the heteroatom in contact with a hydrogen (in Angstrom)
# - epsij_hb = well depth of H-bond (in Kcal/mol)
# - hbond = integer indicating type of H-bonding atom (0=no H-bond)
# - rec_index = initialised to -1, but later on holds count of how many of this atom type are in receptor
# - map_index = initialised to -1, but later on holds the index of the AutoGrid map
# - bond_index = used in AutoDock to detect bonds; see "mdist.h", enum {C,N,O,H,XX,P,S}
#
# - To obtain the Rij value for non H-bonding atoms, calculate the 
#        arithmetic mean of the Rii values for the two atom types.
#        Rij = (Rii + Rjj) / 2
#
# - To obtain the epsij value for non H-bonding atoms, calculate the 
#        geometric mean of the epsii values for the two atom types.
#        epsij = sqrt( epsii * epsjj )
#
# - Note that the Rij_hb value is non-zero for heteroatoms only, and zero for H atoms;
#        to obtain the length of an H-bond, look up Rij_hb for the heteroatom only;
#        this is combined with the Rii value for H in the receptor, in AutoGrid.
#        For example, the Rij_hb for OA-HD H-bonds will be (1.9 + 1.0) Angstrom, 
#        and the weighted epsij_hb will be 5.0 kcal/mol * FE_coeff_hbond.
#
#        Atom   Rii                             Rij_hb       rec_index
#        Type         epsii           solpar         epsij_hb    map_index
#                            vol                          hbond     bond_index
#        --     ----  -----  -------  --------  ---  ---  -  --  -- --
atom_par H      2.00  0.020   0.0000   0.00051  0.0  0.0  0  -1  -1  3    # Non H-bonding Hydrogen
atom_par HD     2.00  0.020   0.0000   0.00051  0.0  0.0  2  -1  -1  3    # Donor 1 H-bond Hydrogen
atom_par HS     2.00  0.020   0.0000   0.00051  0.0  0.0  1  -1  -1  3    # Donor S Spherical Hydrogen
atom_par C      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0    # Non H-bonding Aliphatic Carbon
atom_par A      4.00  0.150  33.5103  -0.00052  0.0  0.0  0  -1  -1  0    # Non H-bonding Aromatic Carbon
atom_par N      3.50  0.160  22.4493  -0.00162  0.0  0.0  0  -1  -1  1    # Non H-bonding Nitrogen
atom_par NA     3.50  0.160  22.4493  -0.00162  1.9  5.0  4  -1  -1  1    # Acceptor 1 H-bond Nitrogen
atom_par NS     3.50  0.160  22.4493  -0.00162  1.9  5.0  3  -1  -1  1    # Acceptor S Spherical Nitrogen
atom_par OA     3.20  0.200  17.1573  -0.00251  1.9  5.0  5  -1  -1  2    # Acceptor 2 H-bonds Oxygen
atom_par OS     3.20  0.200  17.1573  -0.00251  1.9  5.0  3  -1  -1  2    # Acceptor S Spherical Oxygen
atom_par F      3.09  0.080  15.4480  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Fluorine
atom_par Mg     1.30  0.875   1.5600  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Magnesium
atom_par MG     1.30  0.875   1.5600  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Magnesium
atom_par P      4.20  0.200  38.7924  -0.00110  0.0  0.0  0  -1  -1  5    # Non H-bonding Phosphorus
atom_par SA     4.00  0.200  33.5103  -0.00214  2.5  1.0  5  -1  -1  6    # Acceptor 2 H-bonds Sulphur
atom_par S      4.00  0.200  33.5103  -0.00214  0.0  0.0  0  -1  -1  6    # Non H-bonding Sulphur
atom_par Cl     4.09  0.276  35.8235  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Chlorine
atom_par CL     4.09  0.276  35.8235  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Chlorine
atom_par Ca     1.98  0.550   2.7700  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Calcium
atom_par CA     1.98  0.550   2.7700  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Calcium
atom_par Mn     1.30  0.875   2.1400  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Manganese
atom_par MN     1.30  0.875   2.1400  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Manganese
atom_par Fe     1.30  0.010   1.8400  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Iron
atom_par FE     1.30  0.010   1.8400  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Iron
atom_par Zn     1.48  0.550   1.7000  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Zinc
atom_par ZN     1.48  0.550   1.7000  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Zinc
atom_par Br     4.33  0.389  42.5661  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Bromine
atom_par BR     4.33  0.389  42.5661  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Bromine
atom_par I      4.72  0.550  55.0585  -0.00110  0.0  0.0  0  -1  -1  4    # Non H-bonding Iodine


These are the default values that are "baked in" to AutoGrid 4 and AutoDock 4, and are the values that will be used if you do not specify your own parameter file explicitly in your GPF or DPF with the "parameter_file" command.

You can add new atom types and parameters to this file, or modify the existing ones.  If you come up with new or modified parameters, we would like to know about them, so we can incorporate them in future releases.  Thanks!

by morris last modified 2007-07-26 19:11

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