[gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

Phillip Rauscher pmrauscher at uchicago.edu
Tue Apr 4 17:38:57 CEST 2017

Hello all,

I've noticed that in some of the force fields (in the aminoacid.rtp files),
an improper dihedral is applied to the nitrogens in the peptide bond (and
sometimes other amine groups as well), which are all sp3 hybridized with
one lone pair.  Interestingly, the dihedral potential parameters serve to
keep the groups trigonal planar, rather than tetrahedral.  More
specifically, I've seen this in OPLS, Amber03, and Charmm27 - enough to
indicate that it's not a mistake (besides the fact that it's applied to ALL
amino acids!)  The functional form of the improper potential varies between
force fields, but the lowest energy angle is always 0 or 180 indicating
planar structure.

Why is this done?  I've done some digging through the GROMACS publications
as well as those for the force fields and can't seem to find any reference
to this practice?  Is it an attempt to "average out" nitrogen inversions?
Is it just to eliminate a chiral center?

Thanks for your help!

-Phil Rauscher

Phil Rauscher
Graduate Student
de Pablo and Rowan Research Groups
Institute for Molecular Engineering
University of Chicago

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