Because the nitro and trifluoromethyl groups are polar, they should be
equivalenced at the first stage. Doing so at the second stage would cause a
marked deterioration in the quality of the fit around the important polar
areas of these groups.
Second stage equivalencing is only for atoms describing non-polar areas of
the electrostatic potential.
Christopher
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Christopher Bayly, Ph.D.
Research Fellow
Merck Frosst Canada & Co., 16711 Trans-Canada Hwy, Kirkland, Quebec, H9H 3L1
Tel. (514) 428-3403; Fax (514) 428-4900; e-mail bayly_at_merck.com
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> ----------
> From: CRAIG ANTHONY MARHEF[SMTP:CMARHEFKA_at_utmem1.utmem.edu]
> Sent: Friday, January 28, 2000 3:24 PM
> To: amber_at_cgl.ucsf.edu
> Subject: RESP question
> Sensitivity: Confidential
>
> Dear amber users,
>
> I have a question regarding RESP fitting of a small molecule in which
> heavy
> atoms are to have equivalent charges. I have two examples of this in one
> molecule, e.g. a nitro group in which the oxygens are to be equivalent and
> a
> trifluoromethyl group where the fluorines are to be equivalent.
>
> My question is at which stage of a two stage fitting should these atoms be
> made
> equivalent?
>
> Thanks for the input
>
> Craig Marhefka
> Department of Pharmaceutical Sciences
> The University of Tennessee Memphis
> cmarhefka_at_utmem.edu
> 901-448-7530
>
Received on Fri Jan 28 2000 - 12:52:40 PST
