AMBER Archive (2009)

Subject: Re: [AMBER] Re: COOH troubling

From: Jio M (jiomm_at_yahoo.com)
Date: Fri Dec 11 2009 - 13:37:39 CST

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;

JIomm

--- On Fri, 12/11/09, case <case_at_biomaps.rutgers.edu> wrote:

From: case <case_at_biomaps.rutgers.edu>
Subject: Re: [AMBER] Re: COOH troubling
To: "AMBER Mailing List" <amber_at_ambermd.org>
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.

....regards...dac

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