Re: AMBER: Improper angle by Antechamber

From: David A. Case <>
Date: Sun, 28 Jan 2007 18:20:26 -0800

On Sun, Jan 28, 2007, Pavan G wrote:
> I am trying to parameterize a drug and I used antechamber to obtain the
> prepin file. The code found three improper angles [pictures attached. In
> JPEG format and virus-free]. How do I ensure that these are the only three
> improper angles in the system? Why can't atoms C19-C21-C18-C20 or
> C20-C15-C24-C19 form an improper angle? I understand that improper angles
> confine geometry and sometimes determine the chirality of the central atom.

Since the early days of the 80's, Amber force fields have not included
improper torsions at around the common atoms of fused aromatic rings. (If I
am reading your figures correctly, those the the terms of atoms
C19-C21-C18-C20 and C20-C15-C24-C19 you list above.) Antechamber/GAFF
follows this tradition. Vibrational analyses of indole and purines suggested
that these impropers were not needed, but you might want to investigate that
again yourself.

(Junmei may have some comments here...there might have been further
investigations that I am not aware of.)


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Received on Wed Jan 31 2007 - 06:07:15 PST
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