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I have many cases where HTVS docking skips ligands with this error message:


However, if I do the same Glide run using SP mode then this ligand gets docked with no error message. Why does this happen? Is there some parameter I can change to eliminate or reduce this problem?

This ligand rejection message means that all rough-score poses were eliminated during grid-energy minimization. This can occur because forces encountered during minimization drove the ligand outside the grid box, or because the final poses failed the Coulomb-vdW energy cutoff (Output → Advanced Settings → "Reject poses with Coulomb-vdW energy greater than [] kcal/mol," default 0.0).

HTVS retains far fewer intermediate poses than SP, and the minimization schemes are a bit different, so the minimization results certainly could be different. The HTVS poses could be getting rejected because of either the above reasons. You could try increasing the CvdW cutoff energy, to see if some poses can get past the minimization stage. Another alternative is to apply a constraint. You should also look at the rejected ligands, to see how well they are scoring with SP. If they score poorly, then their rejection by HTVS is not a serious problem.

Ultimately, HTVS is a quick method for reducing the number of ligands to process, and necessarily has its limitations. If you do not get satisfactory results with HTVS, you should probably use SP.

Keywords: HTVS, ligand skipped, Glide

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