INDOCK 3.7
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INDOCK is the standard input to DOCK. For DOCK 3.7, the following describes the format expected and options available.
DOCK 3.7 parameter
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# NOTE: split_database_index is reserved to specify a list of files
ligand_atom_file split_database_index #standard for docking large databases
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# OUTPUT
output_file_prefix test. #default, but can be changed
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# MATCHING
match_method 2 #1 matches up to the distance_tolerance below, ignoring match_goal, step, maximum, etc.
#2 uses the adaptive sampling that attempts to get a number of match_goal orientational samples
distance_tolerance 0.05 #starting distance tolerance
match_goal 2500 #desired number of orientational samples to get before quitting under match_method = 2
distance_step 0.05 #increment from distance_tolerance until max or match_goal is reached
distance_maximum 0.5 #biggest tolerance that will be used to attempt to get match_goal orientational samples
timeout 10.0 #number of seconds before quitting on any given ligand
nodes_maximum 4 #max number of points for which all distances must be within the tolerance. 3 possible, 4 suggested.
nodes_minimum 4 #min number of points for which all distances must be within the tolerance. 4 suggested, 3 possible.
bump_maximum 20.0 # stop examining any part of the molecule in which the van der Waals score in kcal/mol exceeds the parameter value
bump_rigid 20.0 #discard the rigid component of the ligand molecule if the van der Waals score in kcal/mol for is above the parameter
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# COLORING
chemical_matching no #default to off, can use chemical matching from DOCK3.6 if desired
case_sensitive no #case sensitivity for chemical matching groups
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# SEARCH MODE
atom_minimum 4 #minimum number of atoms in ligand for it to be scored
atom_maximum 100 #maximum number of atoms in ligand for it to be scored
number_save 1 #how many poses to save. Any number of poses can be saved, but disk space is a factor!
save_limit 1000000 #only scores below (better than) this will have their poses saved. useful for speeding up prospective
#runs, not recommended for retrospective tests as it can influence/hamper result processing.
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# SCORING
ligand_desolvation volume #use GB desolvation scoring, other options are full or none
vdw_maximum 1.0e10 #maximum vdw score possible, prevents overflow
electrostatic_scale 1.0 #scaling factors to be applied to scores, likely not to be trifled with
vdw_scale 1.0 #again, scales the entire vdw score.
internal_scale 0.0 #scales an internal focusing term. set this to 0 as this doesn't work at all/isn't implemented
per_atom_scores no #change to yes if per-atom scoring breakdowns desired. note that this doubles output size.
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# INPUT FILES / THINGS THAT CHANGE
receptor_sphere_file ../dockfiles/matching_spheres.sph #receptor matching spheres file following age old SPH format
vdw_parameter_file ../dockfiles/vdw.parms.amb.mindock #vdw parameter file.
flexible_receptor no #describing only single receptor file for now
total_receptors 1
############## grids/data for one receptor
rec_number 1
rec_group 1
rec_group_option 1
solvmap_file ../dockfiles/ligand.desolv.heavy #GB-based desolvation maps
hydrogen_solvmap_file ../dockfiles/ligand.desolv.hydrogen
delphi_file ../dockfiles/trim.electrostatics.phi #electrostatics map, size must be declared with delphi_nsize below
chemgrid_file ../dockfiles/vdw.vdw #vdw grid file, contains vdw scores
bumpmap_file ../dockfiles/vdw.bmp #vdw bump file, only used for header data for chemgrid_file
############## end of INDOCK
delphi_nsize 193 #size of electrostatics grid (cubic). blastermaster.py trims to the minimum size necessary to save memory.
other indock parameters:
check_clashes yes/no # This parameter is used to check for internal clashes.
# Note that clashes are per-computed during db2 generations
# and stored in the db2 file in the first line for each set (S).
# Read in ligread2.f stored in set_broken variable.
# If check_clash equals yes then all sets with any numbers of clashes (clash number > 0) will not be docked.
http://i.creativecommons.org/l/by-sa/3.0/88x31.png
This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/ This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at https://sites.google.com/site/dock37wiki/.