Hi Priyasha,
I've never used `nastruct` myself so I'm not sure. Looking at the error message you might be missing a "C1" atom your custom nucleotide in your topology/structure? That's the first thing I'd double check/fix.
I'll defer to someone else to answer this.
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 15, 2026, at 7:59 AM, Priyasha Majee <22d0186.iitb.ac.in> wrote:
Thanks a lot Jeremy. It worked perfectly. Also I have a custom nucleotide. In my RNA/DNA duplex, i have a base modification (MOL) in 17th position which is a modified dA. I tried following the instruction on amber hub but it failed for me. Can you help me with this? I would be grateful to you.
The script that i used is:
parm sol-mod.prmtop
trajin prod1000.nc 1 last 10
autoimage
nastruct MyAnalysis \
resrange 1-20 \
naout summary.dat \
resmap MOL:A \
I got the following error:
1: [nastruct MyAnalysis resrange 1-20 naout summary.dat resmap MOL:A ]
Attempting to create custom map for residue MOL
Using residue MOL:17
Trying to map residue MOL to reference A
Found C2
Found N1
Found C4
Found C5
Found N3
Found C6
Found N6
Found C8
New ref base size: 8 atoms.
Set up 20 bases.
----- prod1000.nc (1-100000, 10) -----
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords.
Error: 5' res and/ord 3' res missing C1 atom coords
Thank you
Priyasha
On 2026-04-14 21:50, Leung, Jeremy wrote:
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 Wed Apr 15 2026 - 09:00:03 PDT
