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AD4_parameters.dat
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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 element
# 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 H # Non H-bonding Hydrogen
atom_par HD 2.00 0.020 0.0000 0.00051 0.0 0.0 2 -1 -1 3 H # Donor 1 H-bond Hydrogen
atom_par HS 2.00 0.020 0.0000 0.00051 0.0 0.0 1 -1 -1 3 H # Donor S Spherical Hydrogen
atom_par C 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 C # Non H-bonding Aliphatic Carbon
atom_par A 4.00 0.150 33.5103 -0.00052 0.0 0.0 0 -1 -1 0 C # Non H-bonding Aromatic Carbon
atom_par N 3.50 0.160 22.4493 -0.00162 0.0 0.0 0 -1 -1 1 N # Non H-bonding Nitrogen
atom_par NA 3.50 0.160 22.4493 -0.00162 1.9 5.0 4 -1 -1 1 N # Acceptor 1 H-bond Nitrogen
atom_par NS 3.50 0.160 22.4493 -0.00162 1.9 5.0 3 -1 -1 1 N # Acceptor S Spherical Nitrogen
atom_par OA 3.20 0.200 17.1573 -0.00251 1.9 5.0 5 -1 -1 2 O # Acceptor 2 H-bonds Oxygen
atom_par OS 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2 O # Acceptor S Spherical Oxygen
atom_par F 3.09 0.080 15.4480 -0.00110 0.0 0.0 0 -1 -1 4 F # Non H-bonding Fluorine
atom_par Mg 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 Mg # Non H-bonding Magnesium
atom_par MG 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 Mg # Non H-bonding Magnesium
atom_par P 4.20 0.200 38.7924 -0.00110 0.0 0.0 0 -1 -1 5 P # Non H-bonding Phosphorus
atom_par SA 4.00 0.200 33.5103 -0.00214 2.5 1.0 5 -1 -1 6 S # Acceptor 2 H-bonds Sulphur
atom_par S 4.00 0.200 33.5103 -0.00214 0.0 0.0 0 -1 -1 6 S # Non H-bonding Sulphur
atom_par Cl 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 Cl # Non H-bonding Chlorine
atom_par CL 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 Cl # Non H-bonding Chlorine
atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 Ca # Non H-bonding Calcium
atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 Ca # Non H-bonding Calcium
atom_par Mn 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 Mn # Non H-bonding Manganese
atom_par MN 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 Mn # Non H-bonding Manganese
atom_par Fe 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 Fe # Non H-bonding Iron
atom_par FE 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 Fe # Non H-bonding Iron
atom_par Zn 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 Zn # Non H-bonding Zinc
atom_par ZN 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 Zn # Non H-bonding Zinc
atom_par Br 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 Br # Non H-bonding Bromine
atom_par BR 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 Br # Non H-bonding Bromine
atom_par I 4.72 0.550 55.0585 -0.00110 0.0 0.0 0 -1 -1 4 I # Non H-bonding Iodine
atom_par Z 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 D # Non H-bonding covalent map
atom_par G 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 D # 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 D # 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 D # 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 D # Ring closure Glue Aliphatic Carbon # SF
atom_par W 0.00 0.200 00.0000 -0.00000 0.0 0.0 0 -1 -1 2 O # Acceptor 2 H-bonds Oxygen