Re: [AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Wed, 31 Mar 2010 15:57:42 -0500

Neutral R-NH2 nitrogen is definitely trigonal pyramidal
bond angles H-N-H about 106 and H-N-R about 110.

Considerations regarding neutral N-termini are warranted, since the pKa of
the N-terminal amine is very close to physiologic pH, between 7 and 8, so in
fact the N-terminus has a 50% chance of being neutral in a physiologic
situation. In contrast, the average pKa for the C-terminus carboxyl is
about 4, so the unless one is working under acidic conditions, the carboxyl
is overwhelmingly in the ionized state.


Dean

-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: Dmitri Nilov <nilovdm.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Wed, 31 Mar 2010 09:12:14 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Neutral aminogroup of N-terminal residue: N3 atom type
> choice
> 
> -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
>> 
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> 
> 
> 
> 
> -- 
> Dmitry Nilov,
> Lomonosov Moscow State University
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Mar 31 2010 - 14:00:02 PDT