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Article ID: 755 - Last Modified: May 16, 2011

The core constraints do not seem to constrain the core to where I want it. Is there a way to force Glide to put the core in the right place, and then sort out the rest of the molecule?

The core constraint does apply a restraining potential, but the docking process doesn't anchor the core to the reference position and sample only the side chains. If there are good poses with the core in the desired position, Glide should find them. If it isn't finding good poses, it's possible that the rigid receptor used by Glide is not appropriate for your ligand. You could try superimposing the ligand core on the reference ligand core in Maestro (with Tools → Superpostion), and then running Glide in score-in-place or refinement-only mode. This might give you some indication of why the ligand isn't docking with the constraints. Adding per-residue interactions to this run might give you some further diagnostic clues. If the ligand has clashes with the rigid receptor, you could then try induced fit docking (IFD) to relieve the clash.

Keywords: core constraint, clash, induced fit, IFD, Glide, Maestro

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