# Generating Topology Files for Local Version of Haddock (Large-Scale Protein-Ligand Docking)

**URL:** <https://ask.bioexcel.eu/t/generating-topology-files-for-local-version-of-haddock-large-scale-protein-ligand-docking/5286>\
**Category:** HADDOCK\
**Created:** [October 7, 2024, 8:34pm UTC](https://ask.bioexcel.eu/t/generating-topology-files-for-local-version-of-haddock-large-scale-protein-ligand-docking/5286 "2024-10-07T20:34:53Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![lmullininx3](https://avatars.discourse-cdn.com/v4/letter/l/c0e974/32.png) [@lmullininx3](https://ask.bioexcel.eu/u/lmullininx3)\
**Post date:** [October 7, 2024, 8:34pm UTC](https://ask.bioexcel.eu/t/generating-topology-files-for-local-version-of-haddock-large-scale-protein-ligand-docking/5286/1 "2024-10-07T20:34:53Z")

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I’m working on a project that involves using haddock to dock thousands of protein-ligand complexes on a high-performance computing cluster (the cluster uses slurm). I’m trying to generate the topology files for the ligands.

What is the best way to generate topology and other ligand parameter files locally? Because of the scale of the project, I cannot use a server or API like the ATB server, and PRODGR is down.

Thank you!

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**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [October 8, 2024, 7:01am UTC](https://ask.bioexcel.eu/t/generating-topology-files-for-local-version-of-haddock-large-scale-protein-ligand-docking/5286/2 "2024-10-08T07:01:31Z")

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Dear Lauren,

We are still trying to find a good solution to perform this at high throughput scale, and hope to provide a dedicate tool to perform this for HADDOCK.

But there are solutions you can investigate (but were not benchmarked yet):

- [BioBB ligand parameterization protocol](https://mmb.irbbarcelona.org/biobb/workflows/tutorials/biobb_wf_ligand_parameterization)
- [CCP4 PRODRG local installation](https://www.ccp4.ac.uk/html/cprodrg.html)

I hope these resources will help you !  
Best regards,  
Victor

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**Author:** ![lmullininx3](https://avatars.discourse-cdn.com/v4/letter/l/c0e974/32.png) [@lmullininx3](https://ask.bioexcel.eu/u/lmullininx3)\
**Post date:** [October 8, 2024, 8:05pm UTC](https://ask.bioexcel.eu/t/generating-topology-files-for-local-version-of-haddock-large-scale-protein-ligand-docking/5286/3 "2024-10-08T20:05:16Z")

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I will check those out! Thanks!

Best,  
Lauren