Article ID: 701 - Last Modified: May 16, 2011
Could you explain how the size of the grid box affects the Glide result?
The outer, purple box defines the volume in which the grid potentials are computed. All ligand atoms of a valid pose must be located within this outer box. The inner, green box defines the volume that the ligand center center explores during the exhaustive site-point search. If the ligand is small, its atoms might not reach to the edges of the outer box while its center is constrained to the inner box.
By default, the Glide Grid Generation panel sets the inner box to 10x10x10 and the outer box size according to the size of the native ligand. Usually, this setup would only pose a problem if
1) the active site is very large compared to the ligands being docked, or
2)the native ligand is significantly larger than those that will be docked.
Both situations involve the outer box being too big relative to the inner box when docking small ligands. The inner box size can be visualized and increased via "Advanced Settings" on the Site tab, if necessary.
Keywords: outer box, purple box, inner box, green box, Grid generation panel, box size
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