# Making an index group for the backbone of a single chain

**URL:** <https://gromacs.bioexcel.eu/t/making-an-index-group-for-the-backbone-of-a-single-chain/2662>\
**Category:** User discussions\
**Created:** [August 10, 2021, 12:50pm UTC](https://gromacs.bioexcel.eu/t/making-an-index-group-for-the-backbone-of-a-single-chain/2662 "2021-08-10T12:50:35Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![joshhayden](https://avatars.discourse-cdn.com/v4/letter/j/aeb1de/32.png) [@joshhayden](https://gromacs.bioexcel.eu/u/joshhayden)\
**Post date:** [August 10, 2021, 12:50pm UTC](https://gromacs.bioexcel.eu/t/making-an-index-group-for-the-backbone-of-a-single-chain/2662/1 "2021-08-10T12:50:35Z")

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GROMACS version: 2020.4  
GROMACS modification: No

Hi everyone,

I am wondering, does anyone know a way to make an index group of the backbone atoms of a single chain?

I have conducted an MD simulation of a dimer, and am looking to calculate the RMSD of the backbones of each individual subunit to compare between the two.

Any advice is appreciated!

Josh

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [August 10, 2021, 5:54pm UTC](https://gromacs.bioexcel.eu/t/making-an-index-group-for-the-backbone-of-a-single-chain/2662/2 "2021-08-10T17:54:14Z")

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If you supply `make_ndx` with a `.pdb` or `.tpr` file with chain information, it’s as simple as:

```
> 4 & ch A
```

Otherwise, select based on residue number.