Re: [AMBER] single strand RNA parameters

From: Daniel Roe <>
Date: Thu, 11 Feb 2021 09:28:49 -0500


You're correct, currently the 'nastruct' code is only set up for base
paired calculations. However, it would be relatively simple to apply
the existing calculations (for tilt, shift, etc) to the reference axes
for bases in a single strand. However, I'm not sure whether the
information you get out of it will be useful - someone more
knowledgeable about RNA structure may want to chime in. I'll play
around with the code if I get the time and at least give users the


On Wed, Feb 10, 2021 at 1:41 PM Jorge Iulek <> wrote:
> Dear all,
> Just to be sure, is there a way to use cpptraj to calculate single
> strand (ss) RNA structure parameters with its nastruct tool? As far as
> I understand, it works only for double strand (ds) nucleic acids, right?
> I see that individual torsional angles and ring puckering's can be
> calculated otherwise, but there are some other parameters that would be
> useful for me, like twist, roll, tilt, etc. By the way, this is a ssRNA
> with a number of methylations; residue mapping seems to have worked fine.
> For while, the way out of this I see is to generate pdb coordinates
> of each frame of the trajectory and to use a 3rd part program to do
> that, one example might be x3dna.
> But I wonder of other (maybe easier/more direct way) suggestions.
> Yours,
> Jorge
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Received on Thu Feb 11 2021 - 06:30:02 PST
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