AMBER Archive (2009)

Subject: [AMBER] GAFF atom type question

From: Cen Gao (cengao_at_gmail.com)
Date: Wed Jun 10 2009 - 10:49:00 CDT

Dear Amber users:

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.

Any help is highly appreciated.

Thanks

Cen

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