AMBER Archive (2006)

Subject: Re: AMBER: probable bug in antechamber

From: David A. Case (
Date: Mon Apr 17 2006 - 19:33:35 CDT

On Mon, Apr 17, 2006, David Mobley wrote:

> In particular, nitrogens in some
> rings like pyrrole and indole seem to be misassigned as "na" rather
> than "nc", which seems more appropriate since these are aromatic.

I should let Jumei say something as well, but this is not a simple "bug" or
"misassignment". It is clearly intended that pyrollic nitrogens be assigned
type "na" ("Sp2 N with three substituents", Table 1 in JCC 25:1157, 2004)
rather than type nc ("inner sp2 nitrogen in conjugated ring systems, two
subst."), since there is a hn-na bond defined, but no hn-nc bond. Roughly,
"nc/nd" is intended for pyridine-type nitrogens, not for the bonding situation
one sees in indole or pyrrole.

Indeed, N-methyl pyrrole is one of the "example" compounds shown in Fig. 1 of
the JCC paper (molecule 14 in part (a)), where it is explicitly indicated that
the nitrogen should be type "na". [See also sample molecule 7 in part (b)
of Fig. 1.]

> Is there some reason this shouldn't be considered a failure?

See the arguments above. For better or worse, this is exactly the atom types
that are intended to be assigned here. I'd be surprised if antechamber didn't
make some poor atom type assignments, but it doesn't look to me like this is
one of those cases.


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