Parameter Table

keyword	variable name	allowed values	default
distance_tolerance	dislim	real	1.5
nodes_maximum	nodlim	4 - 8	4
nodes_minimum	lownod	4 - 8	4
ligand_binsize	lbinsz	real	1.0
ligand_overlap	lovlap	real	0.0
receptor_binsize	sbinsz	real	1.0
receptor_overlap	sovlap	real	0.0
bump_maximum	ictbmp	integer	0
focus_cycles	expmax	0 - 3	0
focus_bump	fctbmp	integer	ictbmp
critical_clusters	critdck	yes no	no
mirror_ligands	mirror	yes no discard	no

Parameter Descriptions

distance_tolerance

is the tolerance in Ångstroms for matching ligand-center/ligand-center distances with receptor-center/receptor-center distances. If a negative value is entered, the default value of 1.5 Ångstroms is used. Values smaller or larger than 1.5 are acceptable and should be chosen based on the quality of the structures and the particular application.

nodes_maximum

is the number of ligand-center/receptor-center pairs that DOCK will try to find in generating an orientation. It must be at least 4 so that a unique rotation/translation matrix for orientation can be generated, and must be greater than or equal to nodes_minimum. nodes_maximum defaults to 4 if a smaller value is entered.

nodes_minimum

is the number of ligand-center/receptor-center pairs that DOCK must find in generating an orientation. It must be at least 4 so that a unique rotation/translation matrix for orientation can be generated, and must be less than or equal to nodes_maximum. Values ranging from 4 to 8 are recommended; values greater than 8 may be too restrictive. nodes_minimum defaults to 4 if a smaller value is entered, and defaults to the value of nodes_maximum if a value larger than nodes_maximum is entered.

ligand_binsize

gives the width of the bins containing ligand centers, based on their distance to a "first" center. If the bin width is 1.0 Ångstroms, for example, all centers within 1.0 Ångstroms of the first center are in a bin, all other centers within 2.0 Ångstroms from the first center are in the second bin, and so on. The wider the bins, the more centers in each bin, and the greater the number of matches that will be found. Care should be exercised in setting bin width, since large values may result in excessive output in the case of a SINGLE mode run, and unnecessary slowness in the case of a SEARCH mode run. The number of centers per bin affects time requirements combinatorially, so that performance can degrade rapidly with only a small change in bin width.

ligand_overlap

sets the overlap between ligand bins. Increasing the overlap increases the number of centers per bin, and again the number of matches.

receptor_binsize

is exactly like ligand_binsize, except that the relevant internal distances are now between receptor centers (sphere centers).

receptor_overlap

is exactly like ligand_overlap, except that the relevant internal distances are now between receptor centers (sphere centers).

bump_maximum

gives the maximum number of bad contacts, that is, violations of the close contact limits ccon and polcon, allowed for an orientation to be written out. This is generally set to 0; however, crystal structure complexes occasionally contain atom-atom distances less than those expected based on van der Waals radii. Rather than using larger values for ccon and/or polcon when running distmap, one can increase bump_maximum. Please also see the documentation for rebump.

focus_cycles

specifies the number of nested cycles of "zooming" that can be performed. A value of 0 means that zooming will not be done. When zooming is allowed and DOCK finds an orientation with focus_bump or fewer bad contacts, the widths of the ligand and receptor bins being used are expanded. This increases the fraction of orientations which receive high scores. Again, care must be exercised so that SINGLE mode output does not become excessive. Values of 0 to 2 are recommended.

focus_bump

specifies the maximum number of bad contacts an orientation may have and still induce zooming. Values greater than or equal to bump_maximum are acceptable. Smaller values are automatically set to equal bump_maximum.

critical_clusters

indicates whether to force the usage of particular spheres in generating matches. These spheres are organized into subclusters within standard clusters. One sphere from each defined critical (sub)cluster must be used in creating each valid match. This functionality is further described in the Critical Clusters section. When using critical_clusters it is advisable to set mirror_ligands to discard.

mirror_ligands

dictates how ligand mirror images should be treated. Specifying no means DOCK will not generate ligand mirror images - this is the standard behavior. Specifying yes instructs DOCK to score both real and mirror images of the ligand (note that this option considers ligands not actually in the input file). When mirror_ligands is set to discard, if the mirror image should fit better to receptor spheres than the real image, the ligand orientation is discarded.