How do I generate a grid from a SiteMap binding site?
You can generate a grid from a SiteMap binding site as follows: • Include both the receptor and the desired SiteMap binding site entry in the Workspace. • Open the Receptor Grid Generation panel. • If you are using Schrödinger Suite 2008, choose Entry from the Pick to identify ligand option menu in the Receptor tab; for Schrödinger Suite 2007, choose Molecule. • Pick one of the site points. • Continue with the rest of the grid generation setup, and run the job. The set of site points is likely to produce a default grid box size that is too large if you set the box size by the size of the ligand. You can use the Dock ligands with length <= slider to make the box size more reasonable. If the site is not well defined or the site points extend over a broad region, the center of those points might not be the best place for the grid box center. In that case, you can define the grid box center in terms of selected residues bordering the site, with the Centroid of selected residues option.
