Knowledge Base

Article ID: 570 - Last Modified: August 19, 2014

I need to define a constraint based on distance between the ligand and a few residues. Is it possible to create this constraint?

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 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, which is available from the Scripts menu in Maestro, and also from the command line. You could use a 'contact' filter, with the maximum contact distance set according to the desired NOE constraint distance.

Back to Search Results

Was this information helpful?

What can we do to improve this information?


To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles