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Receptor Grid Generation — Receptor Tab |
Use this tab to define the part of the Workspace structure for which receptor grids should be calculated, and optionally to scale receptor atom van der Waals radii.
This section contains options for defining the part of the system in the Workspace to be treated as the receptor. If only the receptor is included in the Workspace, you can ignore these options.
If the structure in the Workspace is a receptor with a ligand or a SiteMap binding site, use these options to pick the ligand molecule or the site. The ligand or the site will be excluded from receptor grid generation. Everything not defined as the "ligand" is treated as part of the receptor.
If the structure contains a ligand or a SiteMap site as well as a receptor, ensure that this option is selected. If the ligand is a molecule within the ligand/receptor complex entry, choose Molecule from the menu. If the ligand is a separate entry, or if you are using the results of a SiteMap calculation to define the binding site, choose Entry from the menu. Then pick an atom in the ligand molecule or one of the site points. The ligand or site is now distinguished from the receptor.
If this option is selected, when the ligand molecule is picked it is marked with green markers. Deselect the option to remove the markers.
Glide does not allow for flexible receptor docking, but scaling of van der Waals radii of nonpolar atoms, which decreases penalties for close contacts, can be used to model a slight "give" in the receptor and/or the ligand. (Receptor flexibility can be modeled with Glide/Prime Induced Fit docking—see Induced Fit Docking)
You can use the features under Van der Waals radii scaling to scale the van der Waals radii of those receptor atoms defined as nonpolar by a partial charge threshold you can set. For ordinary Glide docking, it is recommended that receptor radii be left unchanged, and any scaling be carried out on ligand atoms. For more on scaling of vdW radii of nonpolar ligand atoms, see the Ligand Docking Panel topic.
This text box specifies the scaling factor: van der Waals radii of nonpolar receptor atoms are multiplied by this value. Because the default is not to scale receptor atom radii, the default value is 1.00.
Scaling of vdW radii is performed only on nonpolar atoms, defined as those for which the absolute value of the partial atomic charge is less than or equal to the number in the text box. Since this is an absolute value, the number entered must be positive. The default for receptor atoms is 0.25.
Select the Use input partial charges option to use partial charges from the input structures instead of those from the force field.
If you want to dock peptides with Glide, select this option to generate grids that are set up for peptide docking. A grid that is prepared for peptides can only be used in the SP-peptide docking mode. (You can dock ligands other than peptides with these grids: no restriction to peptides is applied.)
To perform scaling of van der Waals radii on a per-atom level, or to allow aromatic hydrogen and halogen bonds to be considered, click this button, and make the settings in the Receptor - Advanced Settings dialog box.
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