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Receptor Grid Generation — Site Tab |
In this tab, you use the Center and Size options in this tab to specify the position and the extent of the region for which receptor grids will be calculated.
If the structure in the Workspace consists of a receptor and the ligand molecule you identified in the Receptor Tab, Glide uses the position and size of the ligand to calculate a default center and a default size for the region for which grids will be calculated. When you open the Site tab, the Workspace displays the center of this region as a set of coordinate axes colored bright green, and the boundaries of the region as a purple wireframe cube, called the enclosing box. In any docking job using these receptor grids, ligands are confined to the enclosing box.
If the Workspace structure consists of a receptor only, there is no default center for the enclosing box. The box is not displayed until you have specified a grid center by selecting residues or by supplying its cartesian coordinates.
This option is selected by default, so that the purple enclosing box outline and the green axes at the center are displayed when you enter the tab. Deselect this option to undisplay the box and its center.
Select one of the options under Center to determine how the center of the scoring grid is defined:
This option centers grids at the centroid of the ligand molecule that was defined in the Receptor tab, also called the Workspace ligand. If a Workspace ligand has been defined, this option is the default.
This option centers grids at the centroid of a set of residues that you select. This allows you to define the active site (where grids should be centered) with only the receptor in the Workspace. When this option is chosen, the Specify Residue button becomes available.
The Specify Residues button opens the Active Site Residues dialog box, in which you can pick the residues that best define the active site.
This option centers grids at the specified coordinates. The coordinates of the grid center chosen by any of the other two methods are displayed in these text boxes.
The default Size option is Dock ligands similar in size to the Workspace ligand if you choose Centroid of Workspace ligand for the Center option, and is Dock ligands with length <= if you choose any other Center option.
The first option is suitable when the ligands to be docked are of the same size as, or smaller than, the Workspace ligand. If you expect to dock larger ligands, or if there is no Workspace ligand, select Dock ligands with length <= and use the slider to choose an appropriate maximum ligand length. The slider is set to 20 Å by default.
When you click this button, the Site - Advanced Settings dialog box opens, and the ligand diameter midpoint box is displayed as a cube outlined in bright green. The diameter midpoint of a ligand is the midpoint of the longest line segment that can be constructed between any two atoms in the ligand. The ligand diameter midpoint box is the region in which the diameter midpoint of each docked ligand must remain.
The dialog box allows you to change each dimension of the ligand diameter midpoint box, by moving the slider for the dimension. The default is 10 Å on each side; the sliders covers a range of 6 Å to 14 Å. When you adjust the sliders, the enclosing box also changes size, to keep the distance between the faces of the enclosing box and the ligand diameter midpoint box the same.
A larger ligand diameter midpoint box can be useful to allow ligands to find unusual or asymmetric binding modes in the active site. Conversely, if the default ligand diameter midpoint box allows ligands to stray into regions you know to be unfruitful, you can confine their midpoints to a smaller box, eliminating some of the less useful poses and saving calculation time.
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