How are LigPrep and Confgen different in the way they prepare ligands? Do they do the same thing?

These two programs have different functions. LigPrep converts 2D and 1D molecules into 3D structures, which is crucial for downstream modelling tasks. It works to chemically expand the ligands in terms of the ionization states, tautomers, and steriosomers. More details can be found in the LigPrep User Manual Chapter 1, Introduction and and Section 1.2 which shows all the tasks performed by LigPrep.

ConfGen works to conformationally expand the 3D ligands in terms of the 3D space they occupy. The ConfGen User Manual has details in the Introduction and Section 1.1 and explains how conformations are derived.

So in general, you should run LigPrep first, to prepare 3D structures, and then run ConfGen to generate conformers.

Back to Search Results