# Gmx make\_ndx - index Ca and H instead of N and H

**URL:** <https://gromacs.bioexcel.eu/t/gmx-make-ndx-index-ca-and-h-instead-of-n-and-h/12266>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [June 22, 2025, 3:31pm UTC](https://gromacs.bioexcel.eu/t/gmx-make-ndx-index-ca-and-h-instead-of-n-and-h/12266 "2025-06-22T15:31:17Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![rube23](https://avatars.discourse-cdn.com/v4/letter/r/a8b319/32.png) [@rube23](https://gromacs.bioexcel.eu/u/rube23)\
**Post date:** [June 22, 2025, 3:31pm UTC](https://gromacs.bioexcel.eu/t/gmx-make-ndx-index-ca-and-h-instead-of-n-and-h/12266/1 "2025-06-22T15:31:17Z")

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GROMACS version:2024.5  
GROMACS modification: Yes - PLUMED patched  
I created index for amide groups using `gmx make_ndx -f run.tpr -o amide_index.ndx` and in the prompt entered `aN | aHN`, my understanding is that I have chosen atoms amide nitrogen`N` and attached hydrogen `HN`. However, when I cross checked the indices, they point to `Ca` and `H` respectively for all the atoms pairs. I am not able to understand what is wrong? Is this a known issues or I am missing something?