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AD4.1_bound.dat

by morris last modified 2009-05-29 09:42

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.

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# $Id: AD4.1_bound.dat,v 1.5 2009/03/25 23:50:14 rhuey 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 4.1 Bound
#                    $Revision: 1.5 $

# FE_unbound_model is used to specify how the internal energy of the
# ligand should be treated when estimating the free energy of binding,
# and can be set to one of the following strings:
#   unbound_same_as_bound, extended, or compact
# unbound_same_as_bound -- this assumes the internal energy of the ligand is the
#                          same before and after binding.
# extended -- this assumes the internal energy of the ligand is that of an 
#             extended conformation when unbound.
# compact -- this assumes the internal energy of the ligand is that of a 
#            compact conformation when unbound.
#FE_unbound_model unbound_same_as_bound

# AutoDock 4 free energy coefficients with respect to original (AD2) energetic parameters
#  This model assumes that the bound and unbound conformations are the same.
#  See Table 3 in Huey,Morris,Olson&Goodsell (2007) J Comput Chem 28: 1145-1152.
#
#               Free Energy Coefficient
#               ------
FE_coeff_vdW    0.1662
FE_coeff_hbond  0.1209
FE_coeff_estat  0.1406
FE_coeff_desolv 0.1322
FE_coeff_tors   0.2983

# 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
atom_par Z      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0  # Non H-bonding covalent map
atom_par G      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
atom_par GA     4.00  0.150  33.5103  -0.00052  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aromatic Carbon   # SF
atom_par J      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
atom_par Q      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF

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