-NH2 group is definitely not quite planar, but in classical amber force
field is seems to be parametrized like planar. So, I suppose that usage
of N3 type for NH2 group could cause some inconsistency.
On Wed, Mar 31, 2010 at 5:41 PM, M. L. Dodson <
activesitedynamics.comcast.net> wrote:
> On Wed, Mar 31, 2010 at 02:31:44PM +0400, Dmitri Nilov wrote:
> > Hello, it was discussed at times how to parametrize N-terminal neutral
> > amino acid residue (see for example:
> > http://archive.ambermd.org/200606/0104.html ). R.E.DD.B contributors of
> > N-terminal neutral residue fragments (for example, project F-15) provide
> > script to convert mol2 file to Amber OFF library. But I was confused to
> > notice that they set atom type N3 (sp3 N for charged amino groups) to
> > N-terminal nitrogen. There are no impropers in parm99.dat for N3 to keep
> it
> > planar, while I think that in concept of MM Amber force field neutral
> > aminigroup should be strictly sp2. So what is the reason of N3 choice?
> >
> > Here is an important part of script for NH2-terminal fragment of
> > dimethylalanine N0AI:
> >
> > N0AI = loadmol2 N0AI.mol2
> > set N0AI name "N0AI"
> > # head = null
> > set N0AI tail N0AI.1.C
> > set N0AI.1 connect0 N0AI.1.N
> > set N0AI.1 connect1 N0AI.1.C
> > set N0AI.1 restype protein
> > set N0AI.1 name "N0AI"
> > # set FF atom types
> > set N0AI.1.N type N3
> > set N0AI.1.H1 type H
> > set N0AI.1.H2 type H
> > set N0AI.1.C type C
> > set N0AI.1.O type O
> > set N0AI.1.CA <http://n0ai.1.ca/> type CT
> > set N0AI.1.CB1 type CT
> > set N0AI.1.HB11 type HC
> > set N0AI.1.HB12 type HC
> > set N0AI.1.HB13 type HC
> > set N0AI.1.CB2 type CT
> > set N0AI.1.HB21 type HC
> > set N0AI.1.HB22 type HC
> > set N0AI.1.HB23 type HC
> > # save the OFF library
> > saveoff N0AI N0AI.off
> >
> > Thanks a lot!
> > --
> > Dmitry Nilov,
> > Lomonosov Moscow State University
>
> Some chemist out there can correct me, but I don't think even NH3 ammonia
> is planar. So an unprotonated amine should not be assumed to be planar.
> That is what I have observed with QM minimizations at several levels of
> representation. Anyone care to comment?
>
> Bud Dodson
>
> --
> M. L. Dodson
> Business Email: activesitedynamics-at-comcast-dot-net
> Personal Email: mldodson-at-comcast-dot-net
> Phone: eight_three_two-56_three-386_one
>
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>
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Wed Mar 31 2010 - 07:30:03 PDT
