Subject: nucleotide structures using amber?

From: Jose Manuel Martinez Fernandez <[email-masked]>
Date: Mon, 17 May 1999 10:06:20 +0100 (WETDST)

Dear Netters,

I'm trying to simulate single stranded DNA using
DL_POLY package. Force Field I'm using is AMBER
(JACS'95, vol. 117, 5179-5197)

In order to check if I correctly implemented the FF,
I would appreciate if anyone could send me optimized
structures obtained with other programs and their
corresponding energies using amber95. Just two or three
linked nucleotides I think is enough to test all the
terms.

thanks in advance,
josema

           __________________________________________________________
           _                                                        _
	   _     Jose Manuel Martinez Fernandez, Ph.D.              _
	   _  	Dept. de Quimica Fisica, Universidad de Sevilla     _
	   _  	Facultad de Quimica, SEVILLA 41012, SPAIN           _
	   _     e-mail:  [email-masked]                          _
	   _              [email-masked]                       _
           __________________________________________________________

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From: Konrad Hinsen <[email-masked]>
Date: Mon, 17 May 1999 17:35:04 +0200

> linked nucleotides I think is enough to test all the

It would be even better if someone could provide a publicly accessible
set of test cases. Test cases should be small systems in order to
simplify analysis, and provide as much information about individual
energy terms as possible. Ideally such a set of test cases should be
available for all the popular force fields.
-- 
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