Re: [AMBER] Re: COOH troubling

From: Jio M <>
Date: Fri, 11 Dec 2009 11:37:39 -0800 (PST)

Thanks ,for support and  reply, to Dr. Dean , Dr. Case, Dr. Junmei

I am doing minimisation and dynamics and consulting experimental data. Will reply soon. Sorry for delay from my side.

thanks and regards;


--- On Fri, 12/11/09, case <> wrote:

From: case <>
Subject: Re: [AMBER] Re: COOH troubling
To: "AMBER Mailing List" <>
Date: Friday, December 11, 2009, 1:27 PM

On Fri, Dec 11, 2009, Dean Cuebas wrote:
> All the rings in your system are
> aromatic, with O atom in the aromatic ring, yet no Lewis formula can
> correctly draw that,...

Thanks for your clear explanation.  I just what to emphasize the need to
treat antechamber results with care, especially for unusual structures where
no single Lewis structure suffices; (malachite green also comes to mind here.)
And, of course, thinking carefully about protonation states is also important.


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