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Article ID: 786 - Last Modified:

When docking a ligand with Glide, I get a warning message:

mmlewis warning: Wrong Lewis structure in structure input file

What does this warning indicate?

This warning appears if the ligand lacks hydrogens. Glide requires 3D, all-atom structures with good geometry. PDB structures usually lack hydrogens and higher-order bonds.

We recommend using LigPrep to prepare your ligands. In addition to adding hydrogens and minimizing the structure, it can generate various ionization/tautomer states and stereoisomers. However, to add double bonds, you should use Tools → Assign Bond Orders in Maestro prior to running LigPrep.

Keywords: mmlewis warning, Lewis structure, hydrogens, Glide

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