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

Phillip Rauscher pmrauscher at uchicago.edu
Wed Apr 5 17:45:43 CEST 2017 

I see, thanks for your help!

On Wed, Apr 5, 2017 at 9:27 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> The protonation state is a decision you make in setting up the topology
> (what pH am I modelling?). Having done so, you get whatever amine model the
> force field specifies, and I expect that no force field has such a planar
> amine, because none actually have the improper dihedral you suggest they
> do, for the reason you suggest. :-)
>
> Mark
>
> On Wed, Apr 5, 2017 at 4:10 PM Phillip Rauscher <pmrauscher at uchicago.edu>
> wrote:
>
> > Thanks so much for the reply Mark!  For my own curiosity, is there a way
> > that people generally deal with neutral sp3 Nitogens?  They're chiral
> > centers on simulation time scales, but on macroscopic scales pyramidal
> > inversion eliminates that.
> >
> > On Wed, Apr 5, 2017 at 1:16 AM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Amide nitrogen atoms are trigonal planar because the group is planar.
> > > There's no free rotation about the n-c bond, and the lone pair forms a
> > > hybrid orbital with the carbonyl.
> > >
> > > Mark
> > >
> > > On Tue, 4 Apr 2017 18:05 Phillip Rauscher <pmrauscher at uchicago.edu>
> > wrote:
> > >
> > > > 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
> > > > >
> > > > wrote:
> > > >
> > > > > 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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> > --
> > Phil Rauscher
> > Graduate Student
> > de Pablo and Rowan Research Groups
> > Institute for Molecular Engineering
> > University of Chicago
> > --
> > Gromacs Users mailing list
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-- 
Phil Rauscher
Graduate Student
de Pablo and Rowan Research Groups
Institute for Molecular Engineering
University of Chicago

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