Errors about MMTSB/klust when running CDOCKER flexible docking example files

[waterrr-lxy]

Description:
Hi,
I am having trouble running Flexible_CDOCKER.
When I tried to run the example file in pyCHARMM-Workshop/7CDOCKER_Tutorial/flex/standard_flex.py, it ended with this error

/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 1 -iterate -maxerr 0.01 -mode rmsd -heavy
/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 1 -iterate -maxerr 0.01 -mode rmsd -heavy
double free or corruption (!prev)

I got the same error running the Flexible CDOCKER module in pyCHARMM-Workshop/7CDOCKER_Tutorial/jupyter_lab/cdocker_tutorial.ipynb.
However, running the Rigid CDOCKER module of the notebook seemed to be successful with the following output messages given by MMTSB/kclust:

/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 0.5 -iterate -maxerr 0.01 -mode rmsd -heavy
WARNING: reached 2 clusters
/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 0.6 -iterate -maxerr 0.01 -mode rmsd -heavy
WARNING: reached 2 clusters
/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 0.7 -iterate -maxerr 0.01 -mode rmsd -heavy
WARNING: reached 2 clusters
/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 0.8 -iterate -maxerr 0.01 -mode rmsd -heavy
WARNING: reached 2 clusters
/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 0.9 -iterate -maxerr 0.01 -mode rmsd -heavy
WARNING: reached 2 clusters
/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 1.0 -iterate -maxerr 0.01 -mode rmsd -heavy
WARNING: reached 2 clusters
/data4_large1/home_data/xyli/downloads/MMTSBtoolset/bin/kclust -pdb -centroid -cdist -radius 1.1 -iterate -maxerr 0.01 -mode rmsd -heavy
WARNING: reached 2 clusters

Environment:

charmm version: c48b2
Python : 3.10
OpenMM: 8.1.2
MMTSB toolset was yeseterday installed from github:

https://github.com/mmtsb/toolset

[clbrooksiii]

Hello, we checked this and found that it runs in our environment. I am not sure where the issue is coming from but note that you are using a different OpenMM version (not sure about the other conda environment components. Can you run just this one step with kclust where the error occurs, look at the conformations you are trying to cluster and make sure the structures make sense? What should be present in the pdb files you are clustering are the sidechains you indicated as flexible and the ligand.