AMBER Archive (2009)

Subject: [AMBER] GAFF conjugated ring system dihedrals

From: Floris Buelens (
Date: Wed Jan 28 2009 - 06:04:55 CST

Dear Amber users and force field developers, I have a question relating to the molecule attached (once with GAFF and once with sybyl atom types in mol2 format). Specifically I'm looking at the two bonds, formally single, that link the maleimide (5-membered ring) to the two indole groups. In the GAFF description of these molecules the atom types involved are cc and cd, which are "inner sp2 carbon in conjugated ring systems". Quoting from the GAFF publication (J. Comp Chem. 2004): "Because both cc and cd are inner sp2 carbons in conjugated ring systems, they are assigned according to a simple rule: both cc— cc and cd— cd are conjugated single bonds, and cc— cd is conjugated double bond. [...] The bond parameters and torsional potentials of the two bond types are different. For example, c2— ce or c2— cf or ce— cf double bonds have a v2 of 11.2 kcal/mol, whereas the ce— ce or cf— cf single bonds have a v2 of 5.6 kcal/mol." With reference to the attached structure - one of the bonds is cc-cc, the other is cd-cd, which classifies them as "conjugated single bonds". However the force constant applied is 16 kcal/mol, which is the same as the neighbouring cc-cd bonds and imposes a strong penalty on deviation of the indoles from the plane of the maleimide. Can anyone provide some insights into whether this is representative of the physical reality, or if this could be an artifact resulting from the linking of two conjugated ring systems? thanks a lot, Floris Buelens Crystallography, Birkbeck College, London

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