# Zero protein chain atoms while Indexing a tpr file using gmx 2020 make\_ndx

**URL:** <https://gromacs.bioexcel.eu/t/zero-protein-chain-atoms-while-indexing-a-tpr-file-using-gmx-2020-make-ndx/368>\
**Category:** User discussions\
**Created:** [June 24, 2020, 9:07am UTC](https://gromacs.bioexcel.eu/t/zero-protein-chain-atoms-while-indexing-a-tpr-file-using-gmx-2020-make-ndx/368 "2020-06-24T09:07:02Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![amitsingh](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@amitsingh](https://gromacs.bioexcel.eu/u/amitsingh)\
**Post date:** [June 24, 2020, 9:07am UTC](https://gromacs.bioexcel.eu/t/zero-protein-chain-atoms-while-indexing-a-tpr-file-using-gmx-2020-make-ndx/368/1 "2020-06-24T09:07:02Z")

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GROMACS version: Gromacs 2020.2  
GROMACS modification: No

Hello Everyone,

I found a strange thing while working with Gromacs 2020. I have a .tpr file containing the two protein chain A and B. When I was trying to make an index of chain A and chain B using the gromacs 2020 make\_ndx program, it shows 0 atoms.

Whereas, when I use the gromacs 2018.1 make\_ndx program for the same task, it works and created an index group of protein chain A and chain B.

Please find attached screenshots, one for gromacs 2018 and other while using gromacs 2020. I don’t know whether user forum is a right platform to report this or I need to report this somewhere else. Thank you very much.

 ![gromacs_make_ndx_bug](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/3d073ae38694786c8ae85c54ddc506e530ba2a77.jpeg)

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [June 26, 2020, 3:29pm UTC](https://gromacs.bioexcel.eu/t/zero-protein-chain-atoms-while-indexing-a-tpr-file-using-gmx-2020-make-ndx/368/2 "2020-06-26T15:29:59Z")

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Hi,

Thanks for the report here - the best place to report is

> **[Issues · GROMACS / GROMACS](https://gitlab.com/gromacs/gromacs/-/issues)**
>
> The GROMACS molecular simulation toolkit.

There, it’s also useful to provide the input `.tpr` file.

This is very useful for the development of GROMACS!

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [June 26, 2020, 3:59pm UTC](https://gromacs.bioexcel.eu/t/zero-protein-chain-atoms-while-indexing-a-tpr-file-using-gmx-2020-make-ndx/368/3 "2020-06-26T15:59:42Z")

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There seem to be some more users facing a similar issue, so I went ahead with creating an issue on gitlab here, where you can follow the progress yourself:

> **[Molecule indexing changed in output after simulation (#3575) · Issues ·...](https://gitlab.com/gromacs/gromacs/-/issues/3575)**
>
> Users report that output molecule indices are changed unexpectedly to 1 with a change from GROMACS2019 to GROMACS 2020. \> I switched from 2019 version to the new 2020.2 and...