# How to use Haddock with Grid Engine

**URL:** <https://ask.bioexcel.eu/t/how-to-use-haddock-with-grid-engine/5174>\
**Category:** HADDOCK\
**Created:** [July 5, 2024, 10:41am UTC](https://ask.bioexcel.eu/t/how-to-use-haddock-with-grid-engine/5174 "2024-07-05T10:41:57Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Alba](https://avatars.discourse-cdn.com/v4/letter/a/ea666f/32.png) [@Alba](https://ask.bioexcel.eu/u/Alba)\
**Post date:** [July 5, 2024, 10:41am UTC](https://ask.bioexcel.eu/t/how-to-use-haddock-with-grid-engine/5174/1 "2024-07-05T10:41:57Z")

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Hi, I’m new using Haddock and I’m trying to run the local installation using a queuing system (Grid Engine). I’m not that familiar with queuing systems either. From what I understand, I have to modify the configuration file (QUEUE\_CMD) and the run.cns file (queue\_1), but I don’t know what to write there and if I need to write something specific on the job submission script. I am able to run Haddock using interactive sessions, but it doesn’t generate the models when using qsub. Thank you for the help.

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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:** [July 5, 2024, 3:11pm UTC](https://ask.bioexcel.eu/t/how-to-use-haddock-with-grid-engine/5174/2 "2024-07-05T15:11:43Z")

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You will have to talk to local people to see how to submit to the grid engine.

In the batch-tools directory there is an example of a wrapper script to submit to slurm.

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**Author:** ![AKravchenko](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/akravchenko/32/1168_2.png) [@AKravchenko](https://ask.bioexcel.eu/u/AKravchenko)\
**Post date:** [July 5, 2024, 3:24pm UTC](https://ask.bioexcel.eu/t/how-to-use-haddock-with-grid-engine/5174/3 "2024-07-05T15:24:58Z")

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Also check [this example](https://www.bonvinlab.org/software/haddock2.4/faq/#running-haddock-on-a-cluster-using-a-queuing-system-eg-torque-or-slurm) of running haddock using a queuing system

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**Author:** ![Alba](https://avatars.discourse-cdn.com/v4/letter/a/ea666f/32.png) [@Alba](https://ask.bioexcel.eu/u/Alba)\
**Post date:** [July 5, 2024, 4:01pm UTC](https://ask.bioexcel.eu/t/how-to-use-haddock-with-grid-engine/5174/4 "2024-07-05T16:01:01Z")

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Thank you for the quick response. Once I have the wrapper script, I’ll have to change the run.cns file to provide the path to the wrapper script (queue\_1=‘path/to/wrapper/script’), right?  
How should I modify the configuration file? What should I write for the QUEUE\_CMD?  
Thanks for the help.

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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:** [July 5, 2024, 6:28pm UTC](https://ask.bioexcel.eu/t/how-to-use-haddock-with-grid-engine/5174/5 "2024-07-05T18:28:40Z")

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You can indeed change it in the configuration file and reconfigure.

Or edit the run.cns file in the protocols directory of your current installation and change the queue command.