milot-mirdita
commented
1 year ago It looks like you have openmm 8 installed. I recommend using version 7.7 that should not run into this issue.
Did you install colabfold through the localcolabfold installer? If not please do so, that will install all dependencies that are known to work with each other.
Expected Behavior
Hello ! I installed pdbfixer with conda. There was no error.
Current Behavior
When trying to run pdbfixer with the command line: " pdbfixer ", I get these errors : " Traceback (most recent call last): File "/home/ikram/miniconda3/bin/pdbfixer", line 6, in
from pdbfixer.pdbfixer import main
File "/home/ikram/miniconda3/lib/python3.8/site-packages/pdbfixer/init.py", line 2, in
from .pdbfixer import PDBFixer
File "/home/ikram/miniconda3/lib/python3.8/site-packages/pdbfixer/pdbfixer.py", line 35, in
import openmm as mm
File "/home/ikram/miniconda3/lib/python3.8/site-packages/openmm/init.py", line 24, in
from openmm.openmm import *
File "/home/ikram/miniconda3/lib/python3.8/site-packages/openmm/openmm.py", line 10, in
from . import _openmm
ImportError: /home/ikram/miniconda3/lib/python3.8/site-packages/openmm/../../../libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/ikram/miniconda3/lib/python3.8/site-packages/openmm/../../../libOpenMM.so.8.0)
"
Steps to Reproduce (for bugs)
Please make sure to reproduce the issue after a "Factory Reset" in Colab. If running locally ypdate you local installation
colabfold_batchto the newest version. Please provide your input if you can share it.ColabFold Output (for bugs)
Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.
Context
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Your Environment
Include as many relevant details about the environment you experienced the bug in.