# Loosing chain name in ".pdb" output after mdrun

**URL:** <https://gromacs.bioexcel.eu/t/loosing-chain-name-in-pdb-output-after-mdrun/682>\
**Category:** User discussions\
**Created:** [August 18, 2020, 11:13am UTC](https://gromacs.bioexcel.eu/t/loosing-chain-name-in-pdb-output-after-mdrun/682 "2020-08-18T11:13:37Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![sridharacharya](https://avatars.discourse-cdn.com/v4/letter/s/71c47a/32.png) [@sridharacharya](https://gromacs.bioexcel.eu/u/sridharacharya)\
**Post date:** [August 18, 2020, 11:13am UTC](https://gromacs.bioexcel.eu/t/loosing-chain-name-in-pdb-output-after-mdrun/682/1 "2020-08-18T11:13:37Z")

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GROMACS version: 2020.3  
GROMACS modification: No

I am using “.pdb” as the input and output structure format for my simulation, as I needed some useful features like chain-name.

Gromacs retains the chain information in output “.pdb” structures for many of its commands, but when I run mdrun, the output structure file “.pdb” (the option -c) has lost all chain information. I checked for any options that can be used to preserve chain information, but I found none.

I needed chain information in pdb format structure file, to properly generate index groups.

Is there a way to preserve chain information?

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**Author:** ![maham](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@maham](https://gromacs.bioexcel.eu/u/maham)\
**Post date:** [June 4, 2024, 2:28pm UTC](https://gromacs.bioexcel.eu/t/loosing-chain-name-in-pdb-output-after-mdrun/682/2 "2024-06-04T14:28:52Z")

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Have you gotten any solution?? would appreciate any help

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**Author:** ![fatpmeireles](https://avatars.discourse-cdn.com/v4/letter/f/ecd19e/32.png) [@fatpmeireles](https://gromacs.bioexcel.eu/u/fatpmeireles)\
**Post date:** [June 4, 2024, 3:04pm UTC](https://gromacs.bioexcel.eu/t/loosing-chain-name-in-pdb-output-after-mdrun/682/3 "2024-06-04T15:04:11Z")

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I’m not sure there is a way to preserve chain information in mdrun, but it shouldn’t be necessary for any postprocessing. You can always create new index groups for each one of the chains separately using **gmx make\_ndx** and selecting the appropriate residues/molecules for each chain.