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AD4_PARM99.dat
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AD4_PARM99.dat
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# $Id: AD4_PARM99.dat,v 1.4 2012/01/18 17:45:21 rhuey Exp $
# AutoDock AMBER PARM99 Parameters - Version 1.0
#
# Van der Waals Radii and Epsilon Well-Depths are from AMBER PARM99
# 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 coefficient with respect to original (AD2) parameters
# PREVIOUS to 1/2012:
#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 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
# - Unweighted vdW and Unweighted hbond Well Depths
#
# - To obtain the Rij value for non H-bonding atoms, calculate the
# arithmetic mean of the Rii values for the two atom types.
#
# - To obtain the epsij value for non H-bonding atoms, calculate the
# geometric mean of the epsii values for the two atom types.
#
# - Note that the Rij_hb value is non-zero for heteroatoms only, and zero for H atoms;
# to obtain the Rij_hb for an H-bond, look up for the heteroatom only;
# do not combine Rij_hb values between heteroatoms and hydrogens;
# Similarly, for epsij_hb values.
#
# For example, the Rij_hb for OA-HD H-bonds will be 1.9 Angstrom,
# and epsij_hb will be 5.0 kcal/mol .
#
# Rii Rij_hb rec_index
# Atom epsii solpar epsij_hb map_index
# Type vol hbond bond_index
# -- ---- ----- ----- -------- --- --- - -- -- --
atom_par H 1.20 0.016 0.90 0.00051 0.0 0.0 0 -1 -1 3 # Non H-bonding
atom_par HD 1.20 0.016 0.90 0.00051 0.0 0.0 2 -1 -1 3 # Donor 1 H-bond
atom_par HS 1.20 0.016 0.90 0.00051 0.0 0.0 1 -1 -1 3 # Donor S Spherical
atom_par C 3.81 0.086 29.10 -0.00143 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par A 3.81 0.086 29.10 -0.00052 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par N 3.65 0.170 25.42 -0.00162 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par NA 3.65 0.170 25.42 -0.00162 1.9 5.0 4 -1 -1 1 # Acceptor 1 H-bond
atom_par NS 3.65 0.170 25.42 -0.00162 1.9 5.0 3 -1 -1 1 # Acceptor S Spherical
atom_par OA 3.32 0.210 19.20 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor 2 H-bonds
atom_par OS 3.32 0.210 19.20 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor S Spherical
atom_par F 3.50 0.061 22.45 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par Na 3.73 0.00277 27.30 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par NA 3.73 0.00277 27.30 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Mg 1.59 0.895 2.09 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par MG 1.59 0.895 2.09 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par P 4.20 0.200 38.79 -0.00110 0.0 0.0 0 -1 -1 5 # Non H-bonding
atom_par SA 4.00 0.250 33.51 -0.00214 2.5 1.0 5 -1 -1 6 # Acceptor 2 H-bonds
atom_par S 4.00 0.250 33.51 -0.00214 0.0 0.0 0 -1 -1 6 # Non H-bonding
atom_par Cl 3.90 0.265 30.96 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par CL 3.90 0.265 30.96 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par K 5.31 0.00033 78.66 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Ca 3.43 0.4598 21.06 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par CA 3.43 0.4598 21.06 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Zn 2.22 0.0125 5.58 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par ZN 2.22 0.0125 5.58 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Br 4.44 0.320 45.83 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par BR 4.44 0.320 45.83 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Rb 5.91 0.00017 108.19 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par RB 5.91 0.00017 108.19 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par I 4.72 0.400 54.36 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par Cs 6.79 0.00008 163.91 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par G 4.00 0.086 29.10 -0.00143 0.0 0.0 0 -1 -1 0 # Ring closure Glue Aliphatic Carbon # SF
atom_par GA 4.00 0.086 29.10 -0.00052 0.0 0.0 0 -1 -1 0 # Ring closure Glue Aromatic Carbon # SF
atom_par J 4.00 0.086 29.10 -0.00143 0.0 0.0 0 -1 -1 0 # Ring closure Glue Aliphatic Carbon # SF
atom_par Q 4.00 0.086 29.10 -0.00143 0.0 0.0 0 -1 -1 0 # Ring closure Glue Aliphatic Carbon # SF