# Maximum number of atoms - Refinement interface

**URL:** <https://ask.bioexcel.eu/t/maximum-number-of-atoms-refinement-interface/2251>\
**Category:** HADDOCK\
**Created:** [June 23, 2020, 9:33pm UTC](https://ask.bioexcel.eu/t/maximum-number-of-atoms-refinement-interface/2251 "2020-06-23T21:33:29Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Marija](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marija/32/278_2.png) [@Marija](https://ask.bioexcel.eu/u/Marija)\
**Post date:** [June 23, 2020, 9:33pm UTC](https://ask.bioexcel.eu/t/maximum-number-of-atoms-refinement-interface/2251/1 "2020-06-23T21:33:29Z")

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Hi, I want to run a water refinemet of a protein (44450 atoms) with a cofactor (50 to 100 atoms). I get an error message that the protein PDB exceed the maximum number of atoms allowed on this system, I would like to ask what is the limit of atoms in a system for the Refinemt interface?  
Thank you,  
Marija

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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:** [June 23, 2020, 9:59pm UTC](https://ask.bioexcel.eu/t/maximum-number-of-atoms-refinement-interface/2251/2 "2020-06-23T21:59:27Z")

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The current limit on the 2.2 server is 50000 atoms.  
Does your protein contain all hydrogens when you state 44450 atoms?

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**Author:** ![Marija](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marija/32/278_2.png) [@Marija](https://ask.bioexcel.eu/u/Marija)\
**Post date:** [June 24, 2020, 8:28am UTC](https://ask.bioexcel.eu/t/maximum-number-of-atoms-refinement-interface/2251/3 "2020-06-24T08:28:41Z")

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Thank you very much for your reply. No the initial strucutre which I submit does not contain hydrogens and after protonation there are for sure many more atoms than 50000.  
I would like to ask you what is the atom limit in HADDOCK 2.4? And can I make only a minimization of the strucutre with the HADDOCK 2.4? Because my protein is a membrane protein and I wanted to have energy values for the protein-cofactor interaction after minimization step without subsequent water refinement.  
Thank you very much

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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:** [June 24, 2020, 10:35am UTC](https://ask.bioexcel.eu/t/maximum-number-of-atoms-refinement-interface/2251/4 "2020-06-24T10:35:29Z")

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Hi Maria

The current limit also on 2.4 is 50000, but we will increase to 75000 (including hydrogens).

And the way to set it up is described at: [https://www.bonvinlab.org/software/haddock2.4/tips/advanced\_refinement/](https://www.bonvinlab.org/software/haddock2.4/tips/advanced_refinement/)

By default the option to build the water shell is off and only a minimisation will be done.

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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:** [June 24, 2020, 12:10pm UTC](https://ask.bioexcel.eu/t/maximum-number-of-atoms-refinement-interface/2251/5 "2020-06-24T12:10:51Z")

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> [@Marija](#):
>
> after protonation there are for sure many more atoms than 50000

Just increased to 75 000, could you try again? 🙂