DOCK 3.6 User Manual

From DISI
Jump to: navigation, search

History and Changes

DOCK 3.5 Changes DOCK 3.6

Here is the DOCK 3.5 manual from 1994: DOCK 3.5 Manual

Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see Qnifft DOCK 3.6 conversion for dicussion of this change.

Using Qnifft grids with DOCK 3.5.54 may result in unresonably high electrostatic energies. So be aware of the DOCK version being used and the Electrostatic grids generation method.

Compilation

DOCK Tools

Docking tools


Flexibase Format

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

INDOCK for DOCK 3.6

MPose

Dock Ligand Clustering

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 This has to do with the sphere clusters.
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
mode This parameter has be deprecated. Only the "search" mode is curently used. the "single" mode, which alowed multiple ligand conformations to be saved, was broken and was removed from DOCK 3.6. This fuctionality is in version 3.5 (Mpose binary MPose). The ligand clustering Dock Ligand Clustering code also alows for multiple conformations to be saved.
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

Parameter Name Discription
solvmap_file solvmap_sev is . . .
delphi_file rec+sph2.qnifft.phi is assumed to be gerenerated with qnifft. If delphi grids are used modify delphi_nsize
delphi_nsize defult is 193. if using qnifft grids use defult. if using Delphi grids use 179. see Qnifft DOCK 3.6 conversion for more discution
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