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

Phillip Rauscher pmrauscher at uchicago.edu
Tue Apr 4 18:05:15 CEST 2017

It occurs to me that an example would be helpful.  Here is an excerpt from
the OPLS aminoacids.rtp file detailing alanine:

*[ ALA ] [ atoms ]      N    opls_238   -0.500     1     H    opls_241
0.300     1     CA    opls_224B   0.140     1     HA    opls_140
0.060     1     CB    opls_135   -0.180     2    HB1    opls_140
0.060     2    HB2    opls_140    0.060     2    HB3    opls_140
0.060     2      C    opls_235    0.500     3     O    opls_236
-0.500     3 [ bonds ]     N     H     N    CA    CA    HA    CA    CB
CA     C    CB   HB1    CB   HB2    CB   HB3     C     O    -C     N [
impropers ]    -C    CA     N     H    improper_Z_N_X_Y     CA    +N
C     O    improper_O_C_X_Y *

We can see that the Nitrogen is bound to atoms H, CA, and -C (on the
previous residue).  In the [impropers] section, an improper dihedral is
defined for these four atoms (with the nitrogen in both of the dihedral
planes).  If we look at the definition of that improper in the OPLS
ffbonded.itp file, we see the following:

*[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.; (OPLS
doesnt use impropers for chiral atoms).; Since these functions are periodic
of the form 1-cos(2*x), they are actually; implemented as proper dihedrals
[1+cos(2*x+180)] for the moment, ; to keep things compatible.; The defines
are used in ffoplsaa.rtp or directly in your .top file....; Z -N?-X -Y
improper torsion#define improper_Z_N_X_Y        180.0      4.18400   2*
Given the functional form and the parameters used, this potential has
minima at 0 and 180 degrees, thus keeping all four atoms (centered at the
nitrogen) in the same plane.

On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher <pmrauscher at uchicago.edu>

> 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

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

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