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Is there a limit to the size of the ligands I can dock with Glide?

As of the 2015-1 release, the maximum number of atoms in a ligand is 500, and the maximum number of rotatable bonds is 100. Prior to this release, the limits were 300 atoms and 50 rotatable bonds. For rigid docking and score-in-place, there is no limit on the number of rotatable bonds.

For flexible docking jobs, the number of rotatable bonds can be reduced for some ligands by freezing the amide bonds at their input conformations (choose Retain original conformation from the Amide bonds option menu). This is particularly useful for peptide ligands, which can easily exceed the maximum number of rotatable bonds before the atom limit is reached.

You can reduce the number of rotatable bonds sampled by applying torsional constraints (in the Torsional Constraints tab), using SMARTS patterns to define the torsion. For example, to freeze a peptide backbone, use the SMARTS pattern "C(=O)-NH-C-C(=O)-NH" and constrain all torsions in the pattern.

Keywords: ligand size, restrict

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