Article ID: 655 - Last Modified: May 16, 2011
In the log file, although 10 ligands were docked with none failing, only 4 were written out. Why would this happen?
This could happen if six of the ligands have positive Coulomb-vdW eneriges ('E' or "energy'), as these would get rejected by Glide's energy filter.
If ligands are rejected because of the CvdW energy, it generally means that Glide is having trouble finding good-fitting ligand poses and therefore only poses with some ligand-receptor clashes are produced. This could be due to an enclosed, restricted active site, docked ligands that are larger than the native ligand for the receptor, or induced fit effects. If any of these ligands are the native ligand for this receptor structure or if the ligands you're docking are known actives you might be able to generate alternative receptor conformations (which might be better suited to docking some classes of actives) by running our Glide/Prime Induced Fit Docking workflow.
If you want to see the poses that are getting rejected, you could increase the CvdW energy cutoff under "Advanced Settings" on the Output tab.
Keywords: rejected poses, CvdW energy cutoff, log file, Glide
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