AMBER Archive (2009)

Subject: RE: [AMBER] GAFF atom type question

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jun 11 2009 - 10:43:50 CDT

Hi Cen,

> May I ask a basic question regarding the atom type in GAFF? In
> gaff.dat file, type cc(cd) is described as "Sp2 carbons in non-pure
> aromatic systems", while type ca is labeled as "Sp2 carbons in pure
> aromatic systems". My question is what's the difference between pure
> and non-pure here? I did a google search, it seems that this term was
> mostly used in GAFF.
>
> The original GAFF paper used "inner sp2 carbon in conjugated ring
> system" instead of "non-pure" to describe cc(cd). In that case, does
> non-pure aromatic means a conjugated but non-aromatic ring system?
> However, a recent paper stated that pyrrole is a nonpure aromatic
> system, which confused me.

Junmei can probably comment more here but my interpretation of this is that
by 'pure' it is referring to purely carbon systems, while non-pure refers to
conjugated rings containing N for example. So benzene would be type ca for
all the carbons while in Pyrrole they would be of type cc.

I have not tried this through antechamber to verify if this is indeed the
case but that is my understanding of it, which could of course be completely
wrong. Does the paper describing GAFF expand on this at all?

All the best
ross

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