Article ID: 1172 - Last Modified: May 2, 2012
How do I generate a Glide grid from a SiteMap binding site?
You can generate a Glide 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.
- Choose Entry from the Pick to identify ligand option menu in the Receptor tab. (If you are using Schrödinger Suite 2007 or earlier, 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.
From Suite 2011 on, the Glide Quick Start Guide has an exercise for generating a grid from a site map.
#575: I tried to generate a grid for docking with Glide using the SiteMap output. I got the following warnings. What do the...
#1104: I would like to use a site found by SiteMap as input to Glide docking. How do I do this ?
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