AMBER Archive (2006)

Subject: Re: AMBER: probable bug in antechamber

From: David Mobley (
Date: Tue Apr 18 2006 - 08:52:13 CDT


Great. Thanks. That's reassuring. I guess I should be looking at the
JCC paper rather than the atom type descriptions listed in gaff.dat to
make sense of these.


On 4/17/06, David A. Case <> wrote:
> 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.
> ...regards...dac
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