Article ID: 741 - Last Modified: May 16, 2011
Can I dock bidentate ligands to a metal ion with Glide, and if so, how?
In general, you should be able to dock bidentate ligands to a metal with Glide, using metal constraints. The default ligand feature for a metal constraint is "Charged Acceptor". However, if your ligand has a carboxyl and -OH interacting with the metal (i.e., both neutral), Glide rejects the ligand as being unable to satisfy the constraint. In this case, you should use "Acceptor" as the ligand feature, which covers both charged and neutral acceptor atom types. You should also consider generating metal-binding states with Epik when you prepare your ligands.
If you have trouble getting the correct bidentate interactions with the metal, you could try a modification of our metal scoring and metal constraints that sets the interaction cutoff distance according to the vdW radii of the metal and interacting ligand atoms. To use this feature, write out the Glide Ligand Docking job files, edit the jobname.in file to add the following lines:
and then run the job from the command line:
$SCHRODINGER/glide [options] jobname.in
Keywords: bidentate ligand, docking, constraints, metal, Glide, Maestro
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