I'm doing a grid generation for a protein with a large and very shallow active site. The ends of some of the residues suspected to be important H-bonding species are outside the box. How can I tweak the box so that those ends are inside and can be used as constraints?

If you pick a ligand in the receptor structure, by default the grid box size will be set according to the size of that ligand. If your active site is significantly larger than the ligand, you can switch to "Dock ligands with length <= [] Å" on the Site tab of the Grid Generation panel. With the slider, you can adjust the box size and see it change in the Workspace.

If the active site is much larger than your ligands, you'll probably need to increase the inner (bounding) box, as well. This is under "Advanced Settings" on the Site tab. The maximum inner box size in the GUI is 14 Å, but you can increase it a bit more by editing the jobname.in file, if needed. There is a limit on the number of site points, though, so this inner box can't be too large, or you'll see warning messages about this in the .log file.

Note that the inner and outer boxes don't have to be cubic. If the active site is narrow or shallow, you might be able to decrease one or more dimensions to reduce the overall grid volume.

Keywords: box size, active site, grid size, large site, shallow site, Glide

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