Excluded Volumes from Receptor Dialog Box

Create excluded volumes for a Phase hypothesis from a given receptor or part of a receptor to which the reference ligand of the hypothesis is properly aligned.

To open this dialog box, click Receptor in the Manage Excluded Volumes panel.

  • Using
  • Features
  • Additional Resources

Using the Excluded Volumes from Receptor Dialog Box

The reference ligand of the hypothesis must be positioned properly with respect to the active site of the receptor: for example, the native ligand of the receptor, or a ligand docked by Glide with postminimization.

Placing excluded volumes on all the receptor atoms will result in a large number of excluded volumes, many of which will be far from the ligand. It is usually sufficient to place the excluded volumes only on the receptor atoms that are within a certain distance of the ligand. You can do this by limiting the excluded volume shell thickness.

Another factor to consider is the flexibility of the receptor. If you know that certain side chains in the active site are flexible, you might want to exclude them when you pick the receptor atoms. Or, if you consider all the side chains to be flexible, you might just place excluded volumes on the backbone, or place larger excluded volume spheres on the alpha carbons.

To allow some space for limited receptor flexibility, you can set a minimum distance between the receptor surface and the ligand surface. Spheres are not placed on atoms where the surfaces are closer than this distance. You can also allow for "give" in the receptor by specifying scaling factors for the radii, much like the scaling factors used in Glide to simulate limited receptor flexibility.

Excluded Volumes from Receptor Dialog Box Features

Pick receptor atoms section

Pick atoms to define the part of the receptor that you want to create excluded volumes for, using the picking tools. A sphere is placed on each atom in the receptor, subject to the filtering defined below.

Radii sizes options

Select an option for determining the radii of the excluded volume spheres:

  • Van der Waals radii of receptor atoms—Use the van der Waals radii of the receptor atoms for the radii of the spheres.

  • Fixed radius—Set the radii of the excluded volume spheres to the value supplied in the text box, in angstroms.

  • Atom-level property—Set the radii of the spheres to the value of the atom-level property chosen from the option menu. Atoms with a zero or unspecified value of this property are skipped.

Radii scaling factors options

  • Fixed scaling factor—Set the scaling factor for the excluded volume spheres to the value supplied in the text box, in angstroms. The default is 1.0.

  • Atom-level Maestro property—Set the scaling factor for the spheres to the value in the atom-level Maestro property chosen from the option menu. Atoms with a zero or unspecified value of this property are skipped.

Ignore receptor atoms whose surfaces are within N Å of the ligand surface text box

Excluded volume spheres are not created for receptor atoms whose van der Waals surfaces are within the specified distance of the ligand van der Waals surface.

Limit excluded volume shell thickness to N Å option and text box

Limit the thickness of the excluded volume shell by including spheres only for receptor atoms that are within the given distance of the ligand.

Create Excluded Volumes button

Click this button to run the application that creates the excluded volumes and close the dialog box. When the application finishes, the excluded volumes are added to the table in the Manage Excluded Volumes Panel.

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