Re: [AMBER] Atom-type for aromatic carbon attached by amide nitrogen

From: Aron Broom <>
Date: Tue, 16 Oct 2012 18:21:45 -0400

I don't know what the answer should be, but, as something to add to your
already having considered the PHE carbon, what about in ARG, the terminal
carbon on the sidechain? It is also sp2 hybridized forming a planar group
with its 3 attached heavy atoms, where two of the heavy atoms (the terminal
nitrogens) can be double-bonded as in your ring, and other nitrogen (the
one further back along the sidechain) also has a single hydrogen and is
then bonded to a carbon.

Having said that, isn't GAFF and antechamber supposed to have very generic
types that could handle this? I wouldn't think you'd want to build this
from atom types used for amino acids.


On Tue, Oct 16, 2012 at 3:39 PM, Yun Shi <> wrote:

> Hi everyone,
> What should be the atom type the the [1] carbon (an aromatic carbon
> attached by amide nitrogen) in the picture if parm99.dat is used?
> I understand similar carbon atom in PHE (the aromatic one attached by -OH)
> is of atom type C (sp2 C carbonyl group), but my molecule seems different.
> Thanks for any suggestion,
> Yun
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Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Oct 16 2012 - 15:30:03 PDT
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