# How to separate multiple protein chains in the index file using Gromacs?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-separate-multiple-protein-chains-in-the-index-file-using-gromacs/7301>\
**Category:** User discussions\
**Created:** [October 1, 2023, 8:48am UTC](https://gromacs.bioexcel.eu/t/how-to-separate-multiple-protein-chains-in-the-index-file-using-gromacs/7301 "2023-10-01T08:48:10Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Nik](https://avatars.discourse-cdn.com/v4/letter/n/6de8d8/32.png) [@Nik](https://gromacs.bioexcel.eu/u/Nik)\
**Post date:** [October 1, 2023, 8:48am UTC](https://gromacs.bioexcel.eu/t/how-to-separate-multiple-protein-chains-in-the-index-file-using-gromacs/7301/1 "2023-10-01T08:48:10Z")

</div>

GROMACS version: 2023.1  
GROMACS modification: No

How can I separate multiple protein chains (protein-protein complex structure) in the index file using make\_ndx command?  
Is it necessary to do this after creating the topology or after md simulation (just before analysis of rmsf)?  
Thanks in advance

---

<div class="post-metadata">

**Author:** ![AKA](https://avatars.discourse-cdn.com/v4/letter/a/ba9def/32.png) [@AKA](https://gromacs.bioexcel.eu/u/AKA)\
**Post date:** [October 3, 2023, 1:16pm UTC](https://gromacs.bioexcel.eu/t/how-to-separate-multiple-protein-chains-in-the-index-file-using-gromacs/7301/2 "2023-10-03T13:16:16Z")

</div>

Hello,  
If you have proper chain identifiers, you can use the “chain” option to choose your chain. eg. chain A  
You can also choose the “r” option to select the residues or “a” to choose the atoms. eg. r 10-120