# IndexError: list index out of range while preparing pdb file

**URL:** <https://ask.bioexcel.eu/t/indexerror-list-index-out-of-range-while-preparing-pdb-file/3904>\
**Category:** pmx\
**Created:** [September 15, 2022, 9:32am UTC](https://ask.bioexcel.eu/t/indexerror-list-index-out-of-range-while-preparing-pdb-file/3904 "2022-09-15T09:32:17Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Brijesh](https://avatars.discourse-cdn.com/v4/letter/b/f475e1/32.png) [@Brijesh](https://ask.bioexcel.eu/u/Brijesh)\
**Post date:** [September 15, 2022, 9:32am UTC](https://ask.bioexcel.eu/t/indexerror-list-index-out-of-range-while-preparing-pdb-file/3904/1 "2022-09-15T09:32:17Z")

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![Screenshot from 2022-08-16 23-07-32](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/76319b52e2e2c9f8b957f568d7dd01abb13c3503.png)

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**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\
**Post date:** [September 15, 2022, 9:38am UTC](https://ask.bioexcel.eu/t/indexerror-list-index-out-of-range-while-preparing-pdb-file/3904/2 "2022-09-15T09:38:19Z")

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Did you run the .pdb file through pdb2gmx prior to using pmx?