# Runtime of Docking over 1 week

**URL:** <https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240>\
**Category:** HADDOCK\
**Created:** [April 1, 2023, 5:05am UTC](https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240 "2023-04-01T05:05:15Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![aanushkamehjabin](https://avatars.discourse-cdn.com/v4/letter/a/a88e4f/32.png) [@aanushkamehjabin](https://ask.bioexcel.eu/u/aanushkamehjabin)\
**Post date:** [April 1, 2023, 5:05am UTC](https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240/1 "2023-04-01T05:05:15Z")

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I am trying to perform a protein-protein docking using some altered restrains through the GURU mode. 5 of my docking runs have continued for the past week and they seem to be stuck at it0 99%. Is this the normal running time for such complexes or is there any issues?

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**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [April 1, 2023, 5:44pm UTC](https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240/2 "2023-04-01T17:44:54Z")

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Thanks for reaching out about this issue, could you please share the run ID?

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**Author:** ![aanushkamehjabin](https://avatars.discourse-cdn.com/v4/letter/a/a88e4f/32.png) [@aanushkamehjabin](https://ask.bioexcel.eu/u/aanushkamehjabin)\
**Post date:** [April 3, 2023, 5:35am UTC](https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240/3 "2023-04-03T05:35:05Z")

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Hello, thank you for your reply. This has been resolved. I am now facing another issue where I am getting this error in my input PDB file  
Error in PDB file.  
Issue when parsing the PDB file at line **729**.  
Your PDB contains an Unknown residue **PDBLine: ATOM 729 N HSD A 50 102.158 130.293 -28.820 1.00 0.00 AP1 N** that should be using HETATM record, please check the [HADDOCK library](https://wenmr.science.uu.nl/haddock2.4/library) for a list of supported modified residues.  
Which I am not sure how to resolve

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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 3, 2023, 5:52am UTC](https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240/4 "2023-04-03T05:52:58Z")

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HSD is not an official amino acid name.

Same will apply to HSE. Those should be defined as HIS.

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**Author:** ![aanushkamehjabin](https://avatars.discourse-cdn.com/v4/letter/a/a88e4f/32.png) [@aanushkamehjabin](https://ask.bioexcel.eu/u/aanushkamehjabin)\
**Post date:** [April 3, 2023, 6:09am UTC](https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240/5 "2023-04-03T06:09:03Z")

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Hello,  
Thank you, so in the PDB files should I change the labels from ATOM to HET or change HSD and HSE to HIS

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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 3, 2023, 6:22am UTC](https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240/6 "2023-04-03T06:22:30Z")

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HSD and HSE to HIS

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**Author:** ![aanushkamehjabin](https://avatars.discourse-cdn.com/v4/letter/a/a88e4f/32.png) [@aanushkamehjabin](https://ask.bioexcel.eu/u/aanushkamehjabin)\
**Post date:** [April 3, 2023, 9:01am UTC](https://ask.bioexcel.eu/t/runtime-of-docking-over-1-week/4240/7 "2023-04-03T09:01:02Z")

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Thank you, the issue is resolved.