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Article ID: 580 - Last Modified: June 7, 2011

When running LigPrep on a cyclic peptide with cis amide conformations, the amides stay in the cis conformation rather than changing to trans, which is the correct conformation. How do I fix this?

Since LigPrep is not performing the conversion, you will have to do it manually, before running LigPrep. You can use the QuickTorsion toolbar button - select Convert Cis/Trans from the button menu, and click on an atom in the amide that you want to convert. The geometry of the converted amide will not be very good, so you should run LigPrep afterwards - or you can use the Clean Up Geometry button on the Build toolbar to do a quick minimization first.

Keywords: cis, trans , configurations, Convert Cis/Trans, QuickTorsion toolbar

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