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

From: M. L. Dodson <>
Date: Wed, 31 Mar 2010 08:41:30 -0500

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:
> ). 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 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
> 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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Received on Wed Mar 31 2010 - 07:00:06 PDT
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