# Problem to recognize the .pdb file

**URL:** <https://ask.bioexcel.eu/t/problem-to-recognize-the-pdb-file/3677>\
**Category:** PRODIGY\
**Created:** [April 18, 2022, 8:37am UTC](https://ask.bioexcel.eu/t/problem-to-recognize-the-pdb-file/3677 "2022-04-18T08:37:35Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![decrai60](https://avatars.discourse-cdn.com/v4/letter/d/ac91a4/32.png) [@decrai60](https://ask.bioexcel.eu/u/decrai60)\
**Post date:** [April 18, 2022, 8:37am UTC](https://ask.bioexcel.eu/t/problem-to-recognize-the-pdb-file/3677/1 "2022-04-18T08:37:35Z")

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Hi,  
I want just to derive the free energy change of protein-protein complex, by using a model obtained with the ClusPro program. After sending a .pdb or .mmmCIF file, the Prodigy program send me the following note: "Error during parsing the input sructure: (model.000.01\_WT.pdb - invalid literal for int() with base 10: ““SER””).  
How can I overcome this problem?  
Thank you for your attention

RDC

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**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [April 19, 2022, 7:56am UTC](https://ask.bioexcel.eu/t/problem-to-recognize-the-pdb-file/3677/2 "2022-04-19T07:56:07Z")

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This is likely due to some formatting of the pdb file, please run it over pdbtools’ `pdb_tidy` - [PDB-Tools Web](https://wenmr.science.uu.nl/pdbtools/submit) and trying again.