Comments (2)
lvotapka
commented on June 15, 2024
If the program was working before, this most likely happened because OpenMM 8.0 was installed on top of an existing OpenMM 7.7 installation, or possibly because a SEEKR2 plugin installation from source had a conda-forge installation made overtop it. I'd suggest a clean reinstall of OpenMM and the SEEKR2 plugin, on a fresh conda environment if possible.
If this is happening on a fresh installation from source, make sure you are setting LD_LIBRARY_PATH to point to the OpenMM libraries:
export LD_LIBRARY_PATH="/path/to/bin/openmm/lib:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH="/path/to/bin/openmm/lib/plugins:$LD_LIBRARY_PATH"
from seekr2.
Related Issues (20)
- presimulation check failures and Model Input File HOT 12
- attribute error in analyze.py HOT 3
- query about tutorial simulation time trypsin-benzamidine HOT 9
- errors in seekr2 test HOT 5
- Importance of Target vulnerability for binding kinetics HOT 3
- Non-Uniform Discretization HOT 10
- unable to locate trypsin-benzamidine tutorial page HOT 3
- Convergence Check HOT 36
- error while generating trypsin-benzamidine smd input for hidr HOT 6
- assumptions related to milestoning size/shape interactions in MD region HOT 8
- seekr2 testing error on HPC HOT 16
- BD or MD first with run.py any HOT 25
- error at the convergence step HOT 7
- error in prepare step due to ambpdb output HOT 1
- installing seekr2 on HPC via user account HOT 24
- converge step failure HOT 12
- Build Seekr2 Plugin from source fails HOT 3
- error setting up seekr2 calculation with Heme protein HOT 13
- warnings in prepare.py step HOT 1
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from seekr2.