Hi Priyasha,
You need a space before every line break.
```
nastruct MyAnalysis resrange 1-20\
sscalc\
naout dat\
out nastruct_summary.dat
```
is read as
```
nastruct MyAnalysis resrange 1-20sscalcnaout datout nastruct_summary.dat
```
where as, correctly:
```
nastruct MyAnalysis resrange 1-20 \
sscalc \
naout dat \
out nastruct_summary.dat
```
is read as
```
nastruct MyAnalysis resrange 1-20 sscalc naout dat out nastruct_summary.dat
```
The back slash escapes the line break, but you still need spaces between your terms/arguments (i.e. between 20, sscalc, naout, dat, and out).
Best,
Jeremy L.
---
Jeremy M. G. Leung, PhD
Research Assistant Professor, Chemistry (Chong Lab)
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml230.pitt.edu<mailto:
jml230.pitt.edu> | [He, Him, His]
On Apr 14, 2026, at 11:27 AM, Priyasha Majee via AMBER <amber.ambermd.org> wrote:
I am still getting the same error. Please help.
Regards,
Priyasha
On 2026-04-14 18:41, Rodrigo Galindo-Murillo wrote:
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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Famberhub.chpc.utah.edu%2Fnastruct%2F&data=05%7C02%7CJML230%40pitt.edu%7C0464ec3a81e945d4205a08de9a3a7831%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C639117773109402520%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=83tel2vmAqCSgA378ekb5kQqkjvbZTcdFpZvYiV4IwI%3D&reserved=0
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 - 09:30:02 PDT
