# Pdb\_validate & pdb\_tidy

**URL:** <https://ask.bioexcel.eu/t/pdb-validate-pdb-tidy/5274>\
**Category:** PDB-tools\
**Created:** [September 27, 2024, 2:26pm UTC](https://ask.bioexcel.eu/t/pdb-validate-pdb-tidy/5274 "2024-09-27T14:26:08Z")\
**Posts on this page:** 1\
**Showing post:** 3

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**Author:** ![Beril](https://avatars.discourse-cdn.com/v4/letter/b/6de8d8/32.png) [@Beril](https://ask.bioexcel.eu/u/Beril)\
**Post date:** [October 5, 2024, 11:35am UTC](https://ask.bioexcel.eu/t/pdb-validate-pdb-tidy/5274/3 "2024-10-05T11:35:38Z")

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Hello Professor,

Thank you so much for your reply! I edited manually according to the following link: [PDB format - Plouf](https://cupnet.net/pdb-format/) This was presented in another reply ([Ligand Formatting - #2 by VGPReys](https://ask.bioexcel.eu/t/ligand-formatting/5275/2)) . I edited my ligands accordingly, and now the docking jobs were queued on HADDOCK server successfully. I went back and tried to use PDB-Tools Web once more to check whether I can use validate tool for ligands I generated. I uploaded my pdb and used only pdb\_validate, checked Tidy mark, and clicked Run. I got the following error: " **Last tool output is not PDB format and tidy cannot be applied**" . Then, I used the tool without marking Tidy and got the result. Thank you so much for your time and help!

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