What does LigPrep do by default when processing structures?

By default LigPrep adds hydrogen atoms, removes counter ions, neutralizes the charge on most functional groups, generates up to 8 tautomeric variations per input structure, generates up to 32 stereoisomers per input structure, one low energy ring conformation per stereoisomer and minimizes the energy of all output structures. If an energy-minimized structure is distorted, a short conformational search is performed and the lowest-energy structure produced by that search is retained. In general, LigPrep has a bias towards extended conformations since bound ligands usually adopt extended conformations.

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