# PDB-Tolls install

**URL:** <https://ask.bioexcel.eu/t/pdb-tolls-install/3406>\
**Category:** PDB-tools\
**Created:** [January 15, 2022, 12:23am UTC](https://ask.bioexcel.eu/t/pdb-tolls-install/3406 "2022-01-15T00:23:48Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![pamellac](https://avatars.discourse-cdn.com/v4/letter/p/8edcca/32.png) [@pamellac](https://ask.bioexcel.eu/u/pamellac)\
**Post date:** [January 15, 2022, 12:23am UTC](https://ask.bioexcel.eu/t/pdb-tolls-install/3406/1 "2022-01-15T00:23:48Z")

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Hello, I’m using PDB-Tools to prepare my molecules for an antigen-antibody docking in HADDOCK. I don’t understand how to use the software. The result is a PDB file and a command line. Do I need to install PDB-Tools on linux and run the command line to finally have the archive that will be my input in HADDOCK?

Thank you

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [January 15, 2022, 3:58pm UTC](https://ask.bioexcel.eu/t/pdb-tolls-install/3406/2 "2022-01-15T15:58:09Z")

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Check our antibody-antigen docking tutorial - it describes the use of the PDB-Tools web server:

[https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/#using-pdb-tools-to-extract-the-amino-acid-sequence](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/#using-pdb-tools-to-extract-the-amino-acid-sequence)

Further you can also find instructions to use the command line version of pub-tools in:

[https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/#preparing-pdb-files-for-docking](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/#preparing-pdb-files-for-docking)

And check the PDB-Tools online documentation

[https://www.bonvinlab.org/pdb-tools/](https://www.bonvinlab.org/pdb-tools/)