# Haddock Clustering

**URL:** <https://ask.bioexcel.eu/t/haddock-clustering/3995>\
**Category:** HADDOCK\
**Created:** [November 15, 2022, 7:28pm UTC](https://ask.bioexcel.eu/t/haddock-clustering/3995 "2022-11-15T19:28:43Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![gaurav.sharmapsit](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/gaurav.sharmapsit/32/689_2.png) [@gaurav.sharmapsit](https://ask.bioexcel.eu/u/gaurav.sharmapsit)\
**Post date:** [November 15, 2022, 7:28pm UTC](https://ask.bioexcel.eu/t/haddock-clustering/3995/1 "2022-11-15T19:28:43Z")

</div>

I am new to haddock and trying to run the protein-dna example files in haddock. I am able to run the software. However, I am not sure where do I get the clustered structures.  
Is it in **haddock2.4-2022-01/examples/protein-dna/run1** or in  
**haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/water/analysis** directory?

The last lines of haddock.out file says ===\>  
**Cleaning up HADDOCK run directory**  
**Only files for structure #1 will be kept…**  
\*\* creating file.list in /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/water\*\*  
\*\* creating file.nam in /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/water\*\*  
\*\* creating file.cns in /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/water\*\*  
**starting analysis scripts for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/water**  
\*\* calculating average structure and similarity matrices\*\*  
\*\* queue command:\*\*  
\*\* /bin/csh protein-dna\_run1\_get\_average.job\*\*  
\*\* waiting for the average structure…\*\*

\*\* queue command:\*\*  
\*\* /bin/csh protein-dna\_run1\_fcc\_matrix-water.job\*\*  
\*\* running analysis scripts:\*\*  
\*\* waiting for the matrix file in it1/analysis…\*\*  
\*\* matrix file in it1/analysis is found\*\*  
\*\* running clustering for it1/\*\*  
\*\* Clustering in /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/analysis DONE\*\*  
\*\* Check file /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/analysis /cluster.out\*\*

\*\* waiting for the matrix file in water/analysis…\*\*  
\*\* matrix file in water/analysis is found\*\*  
\*\* running clustering for it1/water\*\*  
\*\* Clustering in /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/water/analysis DONE\*\*  
\*\* Check file /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/structures/it1/water/analysis /cluster.out\*\*  
\*\* Cleaning up the run directory …\*\*  
**##############################################################################**  
**Finishing HADDOCK on: 2022-11-15 13:14:42**  
**Au revoir.**  
**Tot ziens.**  
**Bye bye.**

---

<div class="post-metadata">

**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:** [November 16, 2022, 10:52am UTC](https://ask.bioexcel.eu/t/haddock-clustering/3995/2 "2022-11-16T10:52:55Z")

</div>

You might want to check:

```
https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/#analysing-the-docking-results

```