AMBER Archive (2009)
Subject: Re: [AMBER] GAFF atom type question
From: Cen Gao (cengao_at_gmail.com)
Date: Thu Jun 11 2009 - 19:31:25 CDT
Thanks for the comment. I was thinking originally thinking the same
way, non pure means heterocyclic ring. However, in gaff atom type,
there is an atom type called "nb", which means "Sp2 N in pure aromatic
systems". This makes me thinking that pure doesn't really equals to
Also I have tried to use antechamber to assign atom type to a bunch of
different rings. The result is just not quite consistent so I cannot
really tell. For example, in a fused aromatic ring system like purine,
all atoms on the 6 ring was assigned as pure-aromatic. But atoms on
the 5 member ring was assigned as non-pure.
On Thu, Jun 11, 2009 at 11:43 AM, Ross Walker<ross_at_rosswalker.co.uk> wrote:
> 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
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