The structures that I get back from Epik seem distorted. What can I do about this?

Epik does not always position added hydrogen atoms optimally, resulting in distorted bond angles and inappropriate dihedral angles involving hydrogen atoms. A workaround is to minimize the energy of the generated structures using a program such as MacroModel.

If Epik is used as part of a LigPrep run, the structures are minimized by default, so this problem should not arise.

Keywords: Epik, hydrogens

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