search

choderalab / fah-xchem

Tools and infrastructure for automated compound discovery using Folding@home
MIT License
6 stars 3 forks source link

No module named 'simtk.openmm.app.topology' #160

Open dotsdl opened 2 years ago

dotsdl commented 2 years ago

Observing the following in logs in dev environment:

Exception occurred extracting snapshot from /home/server/server2/projects/13456 data /home/server/server2/data/SVR916310614/PROJ13456 run 943 clone 29 gen 1
No module named 'simtk.openmm.app.topology'

I believe this is related to the use of simtk imports in mdtraj; created mdtraj/mdtraj#1695. May need to resolve to eliminate these, or find a way to avoid the issue.

jchodera commented 2 years ago

With OpenMM 7.6, these imports should move to openmm.app.topology. We can update the imports in fah-xchem, but in codes like MDTraj that need to maintain backward compatibility, we should try both in a try..except. Any chance you could help with this?

dotsdl commented 2 years ago

Yes, I can take this on in mdtraj itself. It needs to happen anyway!

dotsdl commented 2 years ago

This may actually be due to perses; there are imports exactly like the one in the logs above in current master there. We have an existing issue in choderalab/perses#837.