# Can I include pdb chains A and C to index.ndx using Gromacs gmx make\_ndx?

**URL:** <https://gromacs.bioexcel.eu/t/can-i-include-pdb-chains-a-and-c-to-index-ndx-using-gromacs-gmx-make-ndx/1285>\
**Category:** User discussions\
**Created:** [December 17, 2020, 11:22am UTC](https://gromacs.bioexcel.eu/t/can-i-include-pdb-chains-a-and-c-to-index-ndx-using-gromacs-gmx-make-ndx/1285 "2020-12-17T11:22:12Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![paumarc](https://avatars.discourse-cdn.com/v4/letter/p/48db29/32.png) [@paumarc](https://gromacs.bioexcel.eu/u/paumarc)\
**Post date:** [December 17, 2020, 11:22am UTC](https://gromacs.bioexcel.eu/t/can-i-include-pdb-chains-a-and-c-to-index-ndx-using-gromacs-gmx-make-ndx/1285/1 "2020-12-17T11:22:12Z")

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GROMACS version: 2019.2  
GROMACS modification: No

hello everybody,

I am trying to create a Gromacs index using

gmx make\_ndx -f …/inici/AAAKTPVIV\_HLA\_A\_02\_01.pdb -o index.ndx

and I want to include chains A and C to the index

I just tried to do it using the following commands

chain A

chain ‘A’

‘chain A’

etc

but it fails all the time

Found 0 atoms with chain identifier A (idem for C)

Group is empty

Of course, I checked that my PDB has chains A and C (it also has B)

Can any want tell me how to deal with it?

Thanks in advance!

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [December 18, 2020, 8:42am UTC](https://gromacs.bioexcel.eu/t/can-i-include-pdb-chains-a-and-c-to-index-ndx-using-gromacs-gmx-make-ndx/1285/2 "2020-12-18T08:42:17Z")

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HI,  
In 2019 version there was a bug connected to gmx make\_ndx and chain recognition (see release note for 2019.4 [http://manual.gromacs.org/current/release-notes/2019/2019.4.html](http://manual.gromacs.org/current/release-notes/2019/2019.4.html))

Please update to the current version

> **[Downloads — GROMACS 2020.4 documentation](http://manual.gromacs.org/current/download.html)**

or if your work requires 2019 use 2019.6

> **[Downloads — GROMACS 2019.6 documentation](http://manual.gromacs.org/2019.6/download.html)**

Best regards  
Alessandra

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<div class="post-metadata">

**Author:** ![paumarc](https://avatars.discourse-cdn.com/v4/letter/p/48db29/32.png) [@paumarc](https://gromacs.bioexcel.eu/u/paumarc)\
**Post date:** [December 18, 2020, 10:14am UTC](https://gromacs.bioexcel.eu/t/can-i-include-pdb-chains-a-and-c-to-index-ndx-using-gromacs-gmx-make-ndx/1285/3 "2020-12-18T10:14:11Z")

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thank you for your recomendation