Frodo at 18:10, 15 February 2014

2014-02-15T18:10:17Z

← Older revision		Revision as of 18:10, 15 February 2014
Line 56:		Line 56:
	############## end of INDOCK		############## end of INDOCK
	delphi_nsize 47 #size of electrostatics grid (cubic). blastermaster.py trims to the minimum size necessary to save memory.		delphi_nsize 47 #size of electrostatics grid (cubic). blastermaster.py trims to the minimum size necessary to save memory.


			[[Category:DOCK 3.7]]

Rgc at 04:42, 28 March 2013

2013-03-28T04:42:51Z

← Older revision		Revision as of 04:42, 28 March 2013
Line 1:		Line 1:
	This page describes the updates to the [[DOCK3.7]] INDOCK file, alongside a sample file. blastermaster.py described on the [[~~DOCK3~~.7]] page writes an INDOCK file for you, which you can modify.		This page describes the updates to the [[DOCK3.7]] INDOCK file, alongside a sample file. blastermaster.py described on the [[Dock3.7]] page writes an INDOCK file for you, which you can modify.

	DOCK 3.7 parameter		DOCK 3.7 parameter

Rgc at 15:03, 27 March 2013

2013-03-27T15:03:56Z

← Older revision		Revision as of 15:03, 27 March 2013
Line 30:		Line 30:
	atom_maximum 100 #maximum 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!		number_save 1 #how many poses to save. Any number of poses can be saved, but disk space is a factor!
	molecules_maximum ~~10000~~ #how many molecules will be searched before quitting. raise if databases are large.		molecules_maximum 100000 #how many molecules will be searched before quitting. raise if databases are large.
	#####################################################		#####################################################
	# SCORING		# SCORING

Rgc: DOCK3.7 indock file documentation.

2013-03-26T21:55:56Z

DOCK3.7 indock file documentation.

New page

This page describes the updates to the [[DOCK3.7]] INDOCK file, alongside a sample file. blastermaster.py described on the [[DOCK3.7]] page writes an INDOCK file for you, which you can modify.

DOCK 3.7 parameter
#####################################################
# NOTE: split_database_index is reserved to specify a list of files
ligand_atom_file split_database_index #standard for docking large databases
#####################################################
# OUTPUT
output_file_prefix test. #default, but can be changed
#####################################################
# 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 5000 #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 50.0 #van der Waals score in kcal/mol for any part of the molecule to get before further examination stopped
bump_rigid 50.0 #van der Waals score in kcal/mol for the rigid component of the ligand molecule, if above, discarded
#####################################################
# 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
#####################################################
# 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!
molecules_maximum 10000 #how many molecules will be searched before quitting. raise if databases are large.
#####################################################
# 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.
#####################################################
# 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 47 #size of electrostatics grid (cubic). blastermaster.py trims to the minimum size necessary to save memory.

DOCK3.7 INDOCK - Revision history

Frodo at 18:10, 15 February 2014

Rgc at 04:42, 28 March 2013

Rgc at 15:03, 27 March 2013

Rgc: DOCK3.7 indock file documentation.