DOCK 3.5 parameter
################################################.2.A#
######### DOCK 3.6 INPUT PARAMETER FILE #############
##############################################INPUT##
#
receptor_sphere_file          ../../sph/match2.sph
cluster_numbers               1
ligand_atom_file               split_database_index
output_file_prefix            test.
random_seed                   777
#
##############################MATCHING###############
#
distance_tolerance            1.5
nodes_maximum                 4
nodes_minimum                 3
ligand_binsize                0.2
ligand_overlap                0.1
receptor_binsize              0.2
receptor_overlap              0.1
bump_maximum                  1
focus_cycles                  0
focus_bump                    0
focus_type                    energy
critical_clusters             no
#
##############################COLORING###############
#
chemical_matching             yes
case_sensitive                no
#                             ligand color, receptor color
match                         positive negative
match                         positive negative_or_acceptor
match                         positive not_neutral
match                         negative positive
match                         negative positive_or_donor
match                         negative not_neutral
match                         donor acceptor
match                         donor donacc
match                         donor negative_or_acceptor
match                         donor neutral_or_acceptor_or_donor
match                         donor not_neutral
match                         acceptor donor
match                         acceptor donacc
match                         acceptor positive_or_donor
match                         acceptor neutral_or_acceptor_or_donor
match                         acceptor not_neutral
match                         neutral neutral
match                         neutral neutral_or_acceptor_or_donor
match                         ester_o donor
match                         ester_o donacc
match                         ester_o positive_or_donor
match                         ester_o not_neutral
match                         amide_o donor
match                         amide_o donacc
match                         amide_o positive_or_donor
match                         amide_o not_neutral
#
##############################SEARCH MODE###############
#
ligand_desolvation            volume
ratio_minimum                 0.0
atom_minimum                  5
atom_maximum                  60
number_save                   50000
molecules_maximum             300000 
initial_skip                  0
timeout                       20
#
##############################SCORING###################
#
solvmap_file                  ../../grids/solvmap_sev
delphi_file                   ../../grids/rec+sph2.phi
chemgrid_file_prefix          ../../grids/chem
vdw_parameter_file            ../../grids/vdw.parms.amb.mindock
check_clashes                 yes
remove_positive_solvation     no
vdw_maximum                   1.0e10
electrostatic_scale           1.0
vdw_scale                     1.0
#
##############################MINIMIZATION##############
#
minimize                      yes
minimization_max             1.0e15
check_degeneracy              no
simplex_iterations            1000
simplex_convergence           0.1
simplex_restart               1.0
simplex_initial_translation   0.2
simplex_initial_rotation      5.0