Sample INDOCK #1

DOCK 3.5 parameter
#
#       INPUT PARAMETERS
#
mode            single
receptor_sphere_file    4dfr.sph
cluster_numbers         1
ligand_type             c
ligand_atom_file        pter.sto.db
#
#       OUTPUT PARAMETERS
#
output_file_prefix      pter10.sto.nowrt
#
#       MATCHING PARAMETERS
#
distance_tolerance      1.5
nodes_maximum           4
nodes_minimum           4
ratio_minimum           0.0
ligand_binsize          1.0
ligand_overlap          0.2
receptor_binsize        1.0
receptor_overlap        0.2
bump_maximum            0
focus_cycles            0
#
#       SCORING PARAMETERS
#
scoring_option          contact
distmap_file            4dfr.map
# 
#       SINGLE MODE PARAMETERS
#
contact_minimum         60.0
rmsd_override           1.0

Sample INDOCK #2

DOCK 3.5 parameter
#
#       INPUT PARAMETERS
#
mode                    single
receptor_sphere_file    2gbp.rec12.sph
cluster_numbers         1
ligand_type             coordinates
ligand_atom_file        glc.gh.db
#
#       OUTPUT PARAMETERS
#
output_file_prefix      glc.test
#
#       MATCHING PARAMETERS
#
distance_tolerance      0.4
nodes_maximum           4
nodes_minimum           4
ratio_minimum           0.0
ligand_binsize          0.3
ligand_overlap          0.1
receptor_binsize        0.3
receptor_overlap        0.1
bump_maximum            2
# 
#       SINGLE MODE PARAMETERS
#
energy_maximum          -13.0
rmsd_override           0.0
#
#       SCORING PARAMETERS
#
scoring_option          forcefield
vdw_parameter_file      vdw.parms.amb.mindock
chemgrid_file_prefix    2gbp3010
interpolate             yes
minimize                yes

Sample INDOCK #3

DOCK 3.5 parameter
#
#       INPUT PARAMETERS
#
mode                    search
receptor_sphere_file    4dfr.sph
cluster_numbers         1
ligand_type             c
ligand_atom_file        /giga/db/dock3db/cmcall.db3
#
#       OUTPUT PARAMETERS
#
output_file_prefix      cmcall
output_hydrogens        y
#
#       MATCHING PARAMETERS
#
distance_tolerance      1.5
nodes_maximum           4
nodes_minimum           4
ratio_minimum           0.0
ligand_binsize          0.4
ligand_overlap          0.1
receptor_binsize        0.8
receptor_overlap        0.2
bump_maximum            0
focus_cycles            0
#
#       SCORING PARAMETERS
#
scoring_option          contact+forcefield
distmap_file            4dfr.map
vdw_parameter_file      vdw.parms.amb
chemgrid_file_prefix    4dfr3010
interpolate
# 
#       SEARCH MODE PARAMETERS
#
atom_minimum            5
atom_maximum            80
number_save             100
normalize_save          100
molecules_maximum       10000
initial_skip            0
restart_interval        50

Sample INDOCK #4

DOCK 3.5 parameter
#
#       INPUT PARAMETERS
#
mode                    search
receptor_sphere_file    4dfr.sph
cluster_numbers         1
ligand_atom_file        4dfr.db
#
#       OUTPUT PARAMETERS
#
output_file_prefix      4dfr.dock
output_hydrogens        y
#
#       MATCHING PARAMETERS
#
distance_tolerance      1.0
nodes_maximum           5
nodes_minimum           4
ratio_minimum           0.0
ligand_binsize          0.2
ligand_overlap          0.1
receptor_binsize        0.5
receptor_overlap        0.2
bump_maximum            0
critical_clusters
mirror_ligands          discard
#
#       SCORING PARAMETERS
#
scoring_option          contact
distmap_file            4dfr.map
# 
#       SEARCH MODE PARAMETERS
#
atom_minimum            6
atom_maximum            35
number_save             50
normalize_save          0
molecules_maximum       10000
restart_interval        50
# 
#       CHEMICAL MATCHING PARAMETERS
#
chemical_matching
case_sensitive          no
match           hydrophobe hydrophobe
match           acceptor acceptor
match           donor donor
match           hydroxyl donor
match           hydroxyl acceptor
match           minus acceptor
match           plus donor