# Coarse-grained data preprocessing

**URL:** <https://ask.bioexcel.eu/t/coarse-grained-data-preprocessing/3655>\
**Category:** HADDOCK\
**Created:** [April 8, 2022, 10:43am UTC](https://ask.bioexcel.eu/t/coarse-grained-data-preprocessing/3655 "2022-04-08T10:43:23Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ligneoussoar](https://avatars.discourse-cdn.com/v4/letter/l/e495f1/32.png) [@ligneoussoar](https://ask.bioexcel.eu/u/ligneoussoar)\
**Post date:** [April 8, 2022, 10:43am UTC](https://ask.bioexcel.eu/t/coarse-grained-data-preprocessing/3655/1 "2022-04-08T10:43:24Z")

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Dear Haddock team,

We have sucessullly run the basic active/passive with our protein pdb file. When we switched on the coarse-grained method option, it reported error that " There was an error in the topology generation. The most likely cause is an unusual format of your PDB structures.The partial run can be download…". We would like to know how to pre-process our pdb file for the corase-grained method. Thank you!

Best regards,

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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:** [April 8, 2022, 11:22am UTC](https://ask.bioexcel.eu/t/coarse-grained-data-preprocessing/3655/2 "2022-04-08T11:22:27Z")

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I am assuming you are using the web server?

Coarse graining is only available for proteins and nucleic acids.  
Ligand or co-factors are not supported. Check the content of your PDB files

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**Author:** ![ligneoussoar](https://avatars.discourse-cdn.com/v4/letter/l/e495f1/32.png) [@ligneoussoar](https://ask.bioexcel.eu/u/ligneoussoar)\
**Post date:** [April 8, 2022, 12:08pm UTC](https://ask.bioexcel.eu/t/coarse-grained-data-preprocessing/3655/3 "2022-04-08T12:08:18Z")

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Yes, we are working with protein-nucleic acids interaction. The failed run(s) is **132096** and \ ***132097**.