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BrooksResearchGroup-UM / pyCHARMM-Workshop

pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.
MIT License
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Errors about MMTSB/klust when running CDOCKER flexible docking example files #7

Open waterrr-lxy opened 2 months ago

waterrr-lxy commented 2 months ago

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 commented 2 months ago

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.