Hello!
I think you have an extra space or new line in:
"naout dat\
out nastruct_summary.dat"
try with:
"naout nastruct_summary.dat"
Also, at the bottom part of this link:
https://amberhub.chpc.utah.edu/nastruct/
you can find an example on how to include non-canonical nucleotides
for analysis.
Hope that helps!
Rodrigo.
On Tue, Apr 14, 2026 at 5:06 AM Priyasha Majee via AMBER
<amber.ambermd.org> wrote:
>
>
>
> Dear AMBER users and developers,
>
> I want to calculate the standard helical, base-pair and base-step
> parameters for my RNA-DNA hybrid duplex using nastruct command in
> cpptraj. The script I am using is throwing errors:
>
> parm sol-unmod.prmtop
> trajin prod1000.nc 1 last 10
> autoimage
> nastruct MyAnalysis resrange 1-20\
> sscalc\
> naout dat\
> out nastruct_summary.dat
> run
>
> The error is:
>
> Error: [nastruct] Not all arguments handled: [ datout
> nastruct_summary.dat ]
> 1 errors encountered reading input.
>
> I looked up for the correct script, but it's too complicated to
> understand, and there's not much documentation. Please, can someone help
> me with writing the basic script? Also, I have a modification in the DNA
> strand. It's a base modification, so the numbering in the pyrimidine
> ring is completely different from the natural nucleotides. Could you
> tell me how to handle these cases? Which keyword should we use
> specifically to address such modifications? I want to use nastruct for
> both unmodified (wildtype) and modified duplexes. Could someone provide
> a clean Nastruct script for the unmodified and modified duplex?
>
> Thank you
>
> Priyasha Majee
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Received on Tue Apr 14 2026 - 06:30:02 PDT
