Glide One Step Docking

This node performs the Glide grid generation and ligand docking. Settings for Glide are made in this section. If multiple receptors are specified in the input data, the settings are applied to each receptor. This means that the binding site is defined by the same residue specifications for each receptor. For example, if a ligand is used, it must have the same residue name, residue number, and chain ID in each complex.

Backend implementation

Options

Binding Site

Grid center. The center can be specified in one of the following ways:

coords x,y,z

ligand residue-spec

residues residue-spec,residue-spec,...

('residue-spec' should be defined as <Chain ID>:<residue name><residue number>, in case residue is not attached to chain, <Chain ID> should be defined as '_')

where,
coords - specifies the grid center directly
ligand - specifies the centroid of the ligand.
residues - specifies the centroid of the listed residues.

Ligands to dock

List of ligands to dock from the ligand input table. Can take the values all or self (ligand that was last docked with this receptor). The default is "all" for initial docking and should be changed to "self" for redocking.

Size [A]

Dimension of grid enclosing box. Can take the value auto or a number. The value auto computes the box size from the size of the ligand, if the grid is centered on the ligand, or sets it to 26 A if the grid is centered on the centroid of a set of residues.

Receptor vdW scaling

Scaling factor for receptor van der Waals radii.

Ligand vdW scaling

Scaling factor for ligand van der Waals radii.

Reject poses if Coulomb-van der Waals energy is greater than

The default is 100.0 for initial docking and should be changed to 0.0 for redocking.

Reject poses if hydrogen bonding energy is greater than

The default is -0.05 for initial docking and should be changed to 0.0 for redocking.

Redock without H-bond filtering if number of poses found is less than

The default is 1 for initial docking and should be changed to 0 for redocking.

Maximum number of poses per ligand

Maximum number of poses per ligand

Glide Type

Glide docking precision. Can take the values SP or XP.

Generate 4 additional conformations for input to Glide docking

These extra conformations improve the ligand pose. This option is unchecked by default, for initial docking and should be checked for redocking.

Views

Log output of glide-dockingCLI.py

Log output of glide-dockingCLI.py

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