DOCK 3.6 User Manual

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History and Changes

DOCK 3.5 Changes


Compilation

DOCK Tools

Docking tools

Programs, Files, and Protocols

To run DOCK 3.6 for small molcule docking and virtual screening, you need the following:

  • Receptor grid (generated with delphi)
  • Spheres (coloured with )
  • database file containing conformational expantion of your small molecules.

DOCK 3 INPUT FILE and Parameters

Here is an example input file:

 DOCK 3.5 parameter
 ################################################.1.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            1.2
 nodes_maximum                 4
 nodes_minimum                 3
 ligand_binsize                0.3
 ligand_overlap                0.1
 receptor_binsize              0.3
 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                   500
 molecules_maximum             300000 
 restart_interval              10000
 initial_skip                  0
 timeout                       20
 #
 ##############################SCORING###################
 #
 solvmap_file                  ../../grids/solvmap_sev
 delphi_file                   ../../grids/rec+sph2.qnifft.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

Parameters

Parameter Name Discription
receptor_sphere_file Sphere file.
cluster_numbers ??
ligand_atom_file the text file that contains list of 'db.gz' files. Eg. split_database_index
output_file_prefix Output file prefix for the test.
random_seed The Simplex Minimizer requiers a random seed integer. eg.777

SEARCH MODE

Parameter Name Discription
ligand_desolvation volume
ratio_minimum 0.0
atom_minimum 5
atom_maximum 60
number_save 500 (Maxium is 5000)
molecules_maximum 300000
restart_interval 10000
initial_skip 0
timeout 20

DOCK 3 Scoring Function