# Protein-ligand Dock

**URL:** <https://ask.bioexcel.eu/t/protein-ligand-dock/770>\
**Category:** HADDOCK\
**Created:** [February 7, 2018, 1:45am UTC](https://ask.bioexcel.eu/t/protein-ligand-dock/770 "2018-02-07T01:45:39Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![dinesh](https://avatars.discourse-cdn.com/v4/letter/d/a8b319/32.png) [@dinesh](https://ask.bioexcel.eu/u/dinesh)\
**Post date:** [February 7, 2018, 1:45am UTC](https://ask.bioexcel.eu/t/protein-ligand-dock/770/1 "2018-02-07T01:45:39Z")

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hi all,

I am working on protein-ligand docking. i have successfully completed the run but now i have a doubt on the analysis part. in the results, i have a folder called structures under which there are two subfolders it0, it1 and further inside it1 i have a water folder. Each of these folders contain certain energy results. I am quite confused as on to check which folder for my result. Though i understand what each of these folder means, but still am not quite clear to pick which one i should choose for my further studies. It would be really helpful if someone can provide me a clear difference between these folders…

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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:** [February 7, 2018, 4:39pm UTC](https://ask.bioexcel.eu/t/protein-ligand-dock/770/2 "2018-02-07T16:39:29Z")

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It is probably time to start reading some of our HADDOCK papers that describe the entire protocol.  
For example:

[http://www.bonvinlab.org/software/haddock2.2/publications/](http://www.bonvinlab.org/software/haddock2.2/publications/)

and more to be found on our publications web page at: [http://www.bonvinlab.org/publications/](http://www.bonvinlab.org/publications/)  
Some are protocols published in the Methods in Molecular Biology series.

Further the online manual described the various docking stage. See:

[http://www.bonvinlab.org/software/haddock2.2/manual/](http://www.bonvinlab.org/software/haddock2.2/manual/)

it0: contains rigid body docking models  
it1: flexible refinement models  
water: the final, water-refined models and those are the ones used in the server results page