Article ID: 1020 - Last Modified: November 7, 2011
Is there a limit to the size of the ligands I can dock with Glide?
From Suite 2009 on, ligands must have no more than 300 atoms. For flexible docking and refine and score, ligands must have no more than 50 rotatable bonds, but for rigid docking and score-in-place, there is no limit on the number of rotatable bonds. Earlier releases had lower limits, so we recommend that you upgrade your software to take advantage of the higher limits.
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.
From Suite 2010 on, 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: Glide, ligand size, number of atoms, rotatable bonds, torsions, restriction, restrict
#668: Can I dock peptides as ligands in Glide?
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