# How to align pdb? this showed when i processed the pdb

**URL:** <https://ask.bioexcel.eu/t/how-to-align-pdb-this-showed-when-i-processed-the-pdb/559>\
**Category:** HADDOCK\
**Created:** [October 23, 2017, 1:57pm UTC](https://ask.bioexcel.eu/t/how-to-align-pdb-this-showed-when-i-processed-the-pdb/559 "2017-10-23T13:57:56Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Sadia\_Malik](https://avatars.discourse-cdn.com/v4/letter/s/7c8e57/32.png) [@Sadia\_Malik](https://ask.bioexcel.eu/u/Sadia_Malik)\
**Post date:** [October 23, 2017, 1:57pm UTC](https://ask.bioexcel.eu/t/how-to-align-pdb-this-showed-when-i-processed-the-pdb/559/1 "2017-10-23T13:57:56Z")

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First pdb file is incorrectly formatted. Please align the columns of your PDB properly.

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**Author:** ![mtrellet](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/mtrellet/32/42_2.png) [@mtrellet](https://ask.bioexcel.eu/u/mtrellet)\
**Post date:** [October 23, 2017, 2:11pm UTC](https://ask.bioexcel.eu/t/how-to-align-pdb-this-showed-when-i-processed-the-pdb/559/2 "2017-10-23T14:11:23Z")

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Hello Sadia,

Try opening your PDB with a PDB viewer (PyMol, VMD, etc.) and save it through the software and see if you get the same output when running HADDOCK.  
To check the possible cause of errors and have a more verbose output about it, you could try our `pdb_format.py` script available here: [https://github.com/haddocking/pdb-tools](https://github.com/haddocking/pdb-tools)

Good luck,

Mikael