VSW - Receptor Dialog Box

In this dialog box you specify the options for reading or generating the receptor grids. In addition, you can select constraints to be used in docking to the receptor, and provide an identifier and a GlideScore offset.

To open this dialog box, click Add or Edit in the Receptors tab of the Virtual Screening Workflow panel.

  • Features
  • Additional Resources

VSW - Receptor Dialog Box Features

Grid source options

There are two options for specifying the grid source:

  • File—Read the grid from file. Enter the path to the grid file in the text box, or click Browse and navigate to the file, which can be of type .grd or .zip.

  • Generate from Workspace—Generate a new grid, using the structure that is in the Workspace. This structure must be a properly prepared protein with a ligand, and can come from a single entry for the complex or separate entries for the protein and the ligand. See the Protein Preparation Workflow Panel topic for information on protein preparation. When you select this option, the controls for setting up the grid are activated:

    Pick to identify ligand option

    Pick the ligand in the Workspace. The ligand is excluded from the structure when the grids are generated, and is used to define the enclosing box center if the Centroid of Workspace ligand option is selected.

    Center options

    Specify the grid center. The options are:

    • Centroid of Workspace ligand—use the centroid of the ligand to define the enclosing box center.
    • Centroid of selected residues—use the centroid of the selected residues to define the enclosing box center. Click Select to select the residues, which are then listed in the text box. This button opens the Atom Selection Dialog Box.
    • Supplied X,Y,Z coordinates—use the coordinates given in the text boxes as the enclosing box center.
    Dock ligands with length slider

    Use this slider to specify the maximum size of ligands to be docked. This value determines the size of the enclosing box.

    Delete all waters option

    Select this option if you want to delete all waters from the protein before making the grid.

    Create grids for all water combinations option

    Generate grids for each number and combination of water molecules that are explicitly included with the receptor, so that you can dock the ligands with all possible combinations of structural waters. The number of grids increases exponentially with the number of water molecules, so you should take care to only include critical waters.

Constraints button

Opens the VSW - Receptor Constraints Dialog Box in which you can specify the constraints to be used in docking for the receptor. The constraints specified here include constraints that are included with the receptor grid and constraints on the ligand core. You can define and use positional, NOE, H-bond, and metal constraints. Hydrophobic constraints cannot be defined or used here. You can set up constraints for grids that are to be generated, you can request the use of constraints for both pregenerated and new grids. You can add constraints to a receptor by picking in the Workspace.

Receptor identifier text box

Enter an identifier for the receptor. This is listed in the Receptors for docking table as the Receptor ID. The default is to use a numeric index.

GlideScore offset text box

Enter the offset to be applied to the GlideScore for this receptor. This offset can be used to compare GlideScores between receptors.

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