# Haddock3 Doesn't Recognize clustrmsd Module After the Update

**URL:** <https://ask.bioexcel.eu/t/haddock3-doesnt-recognize-clustrmsd-module-after-the-update/4866>\
**Category:** HADDOCK\
**Created:** [March 1, 2024, 3:28pm UTC](https://ask.bioexcel.eu/t/haddock3-doesnt-recognize-clustrmsd-module-after-the-update/4866 "2024-03-01T15:28:38Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![YFeri](https://avatars.discourse-cdn.com/v4/letter/y/b4bc9f/32.png) [@YFeri](https://ask.bioexcel.eu/u/YFeri)\
**Post date:** [March 1, 2024, 3:28pm UTC](https://ask.bioexcel.eu/t/haddock3-doesnt-recognize-clustrmsd-module-after-the-update/4866/1 "2024-03-01T15:28:38Z")

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Hello,  
I recently updated the Haddock3 repository to incorporate the ilrmsdmatrix module for my ab-initio protein-protein docking. However, since the update, Haddock3 is no longer capable of recognizing the clustrmsd module when I run the command “haddock3 config\_file.cfg.” I encounter the following error:  
[2024-03-01 09:52:36,126 libutil ERROR] The following parameters do not match any expected parameters for module ‘clustrmsd’: ‘threshold’ did you mean ‘ncores’?.

Interestingly, when I run “haddock3-cfg -m clustrmsd,” it runs smoothly and is able to recognize the module.  
[clustrmsd]  
criterion = ‘distance’ # $minchars 0 / $maxchars 100 / $title Criterion for fcluster / $short Criterion to be used to cut the dendrogram / $group analysis / $choices [‘distance’, ‘maxclust’]  
linkage = ‘average’ # $minchars 0 / $maxchars 100 / $title Linkage type / $short How to lump together clusters in hierarchical clustering / $group analysis / $choices [‘average’, ‘centroid’, ‘complete’, ‘median’, ‘single’, ‘ward’, ‘weighted’]  
min\_population = 4 # $min 1 / $max 9999 / $title Clustering population threshold / $short Threshold employed to exclude clusters with less than this number of members. By default 4. / $group analysis  
clust\_cutoff = 7.5 # $min 1 / $max 9999 / $precision 3 / $title Clustering cutoff distance / $short Value of cutoff cophenetic distance. / $group analysis  
n\_clusters = 4 # $min 1 / $max 9999 / $title Number of clusters / $short Number of clusters to be formed / $group analysis

Thank you.

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<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:** [March 1, 2024, 3:40pm UTC](https://ask.bioexcel.eu/t/haddock3-doesnt-recognize-clustrmsd-module-after-the-update/4866/2 "2024-03-01T15:40:57Z")

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We have renamed some parameters to make them clearer…

In your case you need to replace threshold by min\_population

Check the examples