History and Changes
DOCK 3.5 Changes
DOCK 3.6
Here is the DOCK 3.5 manual from 1994: DOCK 3.5 Manual {LINK NO LONGER WORKING}
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
|