Article ID: 570 - Last Modified: May 13, 2011
I need to define a constraint based on distance between the ligand and a few residues. Would it be possible to create this constraint and add a potential?
You can apply distance (NOE) constraints in Glide, as of Suite 2011. These constraints are included with the positional constraints in the Positional/NOE tab of the Receptor Grid Generation panel.
In Suite 2010 and earlier, Glide doesn't support distance constraints, but you can achieve something similar with positional constraints centered at specific receptor atoms. Positional constraints don't have a default ligand feature that can satisfy them (as do Hydrophobic or H-bond constraints), so you'll need to define the ligand feature yourself via "Edit Feature". It isn't possible to set the constraint potential in Glide: Glide constraints are mainly, but not entirely, filters on acceptable poses at various stages of the docking process.
Another option would be to generate poses with Glide without constraints, and then apply a post-docking filter to identify those with the desired ligand-receptor distances. This can be done with the "Pose Filter" script from our website (Resources & Downloads → Script Center, in the Docking section). This script can be run as a panel in Maestro (via the Scripts menu) or from the command line. You could use a 'contact' filter, with the maximum contact distance set according to the desired NOE constraint distance.
Keywords: docking constraint, positional constraints, distance constraints, Glide
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