Article ID: 927 - Last Modified: May 1, 2012
I would like to use Glide to dock to an RNA molecule that is rather large. How can I generate a grid for my target?
From Suite 2010 on, Glide supports up to 90,000 atoms in the receptor. If the RNA target is too large, you might have to truncate it for use with Glide. You can do this as follows:
not (atom.selected or withinbonds 1 (atom.selected and atom.ele P))
The purpose of this expression is to complete the phosphates, which are cut between the P and the O, and then invert to delete the atoms that aren't selected.
Keywords: RNA, Glide, docking
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