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

From: Mohaddeseh Habibzadeh <>
Date: Sun, 27 Nov 2016 21:26:59 +0330

 Hello doctor
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.
Once I used nab according to the program input file, which I just could mention the sequence there, but no secondary structure.
It is important for me to have the relation between different RNA structures. Otherwise the program made reasonable pseudoknot.pdb.
thanks and Regards

On Sun, 11/27/2016 12:40 PM, David A Case <> wrote:
> On Sun, Nov 27, 2016, Mohaddeseh Habibzadeh wrote:
> > I want to have a NAB input file containing first and second structure of RNA.
> > Is there any way to make the pdb file of third structure of RNA by this?
> We need lots more information and context. What is the "NAB input file"?
> What are the "first", "second" and "third" RNA structures?
> Don't be afraid to experiment. Generally, showing exactly what you tried,
> and showing what the result was, is the best way to get specific help.
> ....dac
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Received on Sun Nov 27 2016 - 10:00:03 PST
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