[gmx-users] Search more information of Atom type: N inside the R-N(CH3)3

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 22 17:29:58 CEST 2008

Chih-Ying Lin wrote:
> Hi
> What is the atom type of Nitrogen inside the molecule  R-N(CH3)3  ?
> I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers.
> There are 6 atom types for Nitrogen.
> N         peptide nitrogen (NH)
> NT       terminal nitrogen (NH2)
> NL       terminal nitrogen  (NH3)
> NR      aromatic nitrogen
> NZ      Arg NH (NH2)
> NE      Arg NE (NH)
> My understanding is either NT or NL but not sure which is the exact one.
> Could anyone direct me about the decision of the atomic type?

Difficult to say, because IIRC no -N(CH3)3 exists within Gromos96.  Probably the 
closest atom type is NL, based on its hybridization state and the charged nature 
of the group in question.


> Thank you
> Lin
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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