AMBER Archive (2009)

Subject: Re: [AMBER] GAFF atom type question

From: Cen Gao (cengao_at_gmail.com)
Date: Sun Jun 14 2009 - 23:12:19 CDT

First sorry for the spam. I am resending my last email plus some
additional comments at the end, as I am having trouble to send my mail
to amber mail list for a while. I have to resend it several times to
let it go through. Does anyone else have the same problem?

Hi Ross:
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
non heterocyclic.

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.

Also the definition varies quite a bit from different resources.
Taking atom type "nc (nd)" as an example,
The gaff.dat file in amber package describes this as "Sp2 N in
non-pure aromatic systems"
The original gaff paper refers it as "nc(nd) inner sp2 nitrogen in
conjugated ring systems, 2 subst."
However, the GAFF website
(http://ambermd.org/antechamber/gaff.html#atomtype) lists this type as
"inner sp2 N in conj. chain systems" So I don't know which one is the
latest one that I can trust.

Thanks

Cen

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
> ross
>
>
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