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 | [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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7CJML230%40pitt.edu%7C0464ec3a81e945d4205a08de9a3a7831%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C639117773109428210%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=vvQ%2B%2FLVyoruK%2FhGLaZg%2FsAiV3A9wHqT%2FhCIz5buEaQk%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7CJML230%40pitt.edu%7C0464ec3a81e945d4205a08de9a3a7831%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C639117773109447131%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2BjOwk6MX2Em95FIWmXUQW8O0Scc1qVZ043U%2Bd8R97Eo%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 15 2026 - 05:30:02 PDT
