Article ID: 917 - Last Modified: December 4, 2010
I am modeling NADH in a protein complex, and I find that a nicotinamide ring is in a boat configuration with OPLS_2001 but is planar with OPLS_2005. Why the difference, and which is correct?
The nicotinamide ring is close to planar in most structures, but has a soft out-of-plane deformation mode. OPLS_2005 recognizes the conjugation in this system, which OPLS_2001 does not, so you should use OPLS_2005.
Keywords: force field, ring conformation
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