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Is there a way to increase the maximum rotatable bonds allowed in Glide?

You cannot increase the number of rotatable bonds beyond 100. Docking becomes increasingly difficult the more flexible the ligand becomes, due to the enormous ligand conformational space involved. However, there are several alternatives that will allow you to dock molecules that have more that this number of rotatable bonds.

If you are docking peptide ligands, you can decrease the number of rotatable bonds that are counted by Glide by freezing amide bonds at their input conformations, in the Settings tab of the Ligand Docking panel (for "Bias sampling of torsions for" select "Amides only" and choose "Retain original conformation").

You can apply torsional constraints to freeze parts of the ligand structure, so that the rest of the structure has 100 or fewer rotatable bonds.

A third alternative is to generate ligand conformations outside Glide and dock each of these conformations rigidly as a separate ligand. You could generate the conformations with ConfGen or MacroModel, for example. If you have a Phase database with ligand conformers, you can dock them with VSW or (as of the 2015-1 release) Glide.

If you are using a release earlier than 2015-1, the limit is 50 rotatable bonds, and you should consider upgrading to a more recent release.

Keywords: peptide-protein

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