Re: [AMBER] NAB input file containing first and second structure of RNA

From: Mohaddeseh Habibzadeh <>
Date: Mon, 28 Nov 2016 13:02:20 +0330

That' OK. Then I can not use NAB for this goal.
Thanks for your suggestion but since I know Rosetta does not need secondary structure to run RNA structure modeling.
Best Regards

On Sun, 11/27/2016 04:06 PM, David A Case <> wrote:
> On Sun, Nov 27, 2016, Mohaddeseh Habibzadeh wrote:
> > The RNA sequence is the first structure in my mind, the secondary
> > structure of RNA which is showing by parenthesis and dots ((..)) .
> > I want to make a tertiary RNA structure (pseudoknot form) with my desire
> > secondary structure.
> OK: I sort of understand now. NAB doesn't include anyway to process secondary
> structure designiations like '((..))'. I think you should explore other
> possibilities (e.g. Rosetta), although the general problem of going from a
> secondary structure description to 3D coordinates is very much an unsolved
> problem. But NAB is not equipped to help very much with this: you could
> expand the psedoknot code, but those are ideas from 20 years ago, and other
> programs in that area have progressed a lot since then.
> ....dac
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Received on Mon Nov 28 2016 - 02:00:05 PST
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