Article ID: 564 - Last Modified: January 4, 2012
Is there a way to increase the maximum rotatable bonds allowed in Glide to higher than 50?
No, you cannot increase the number of rotatable bonds beyond 50. 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.
Beginning with Suite 2010, you can apply torsional constraints to freeze parts of the ligand structure, so that the rest of the structure has 50 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 by using VSW.
Keywords: max rotatable bonds, peptide-protein , docking, Glide, torsional constraints
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