Article ID: 666 - Last Modified: December 4, 2010
I seem to be getting a lot of errors, and more than half of my molecules aren't docked. What could be wrong?
If more than half of the ligands are failing to dock, there probably is something wrong with the job setup. Some possibilities are:
1)There is a ligand in the active site (not 'picked' during Grid Generation setup) that is blocking the docking of other molecules;
2)The grid box is too small (perhaps because the 'picked' ligand was much smaller than the ligands you're trying to dock;
3) The ligands haven't been prepared properly (e.g., with LigPrep), and are getting rejected because of lack of hydrogens, unsupported atoms, or poor geometry;
4) You've set a low maximum ligand size;
5) You're applying constraints that can't be satisfied by most molecules.
Keywords: docking failure, ligands, job setup
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