AMBER Archive (2006)

Subject: Re: AMBER: double stranded polyribocytidylic acid

From: Bill Ross (
Date: Thu Feb 16 2006 - 12:53:10 CST

> > What I found suspicious in Kateryna's description is the
> > vertical distance of base pairs 3.11 A, since each base
> > pair is protonated, and thus I would expect increased
> > vertical separation.
> The value 3.11 A was taken from the Langridge and Rich work, as I've
> not found any other information about the helical structure of double
> stranded polyrC. I'll try to vary rise and twist to build some other
> models.

Possibly dynamics will find a more separated stack for you.
I am a great fan of using 10K dynamics in vacuum to explore the
nearby configurations once the major kinks have been solved.

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