Problems runing rbfe tutorial

[dkchalmers]

Hi All,

I am running the RBFE CLI tutorial using the SLURM script given under 'Running the simulations' here https://docs.openfree.energy/en/v1.0.0/tutorials/rbfe_cli_tutorial.html

I have installed the developer version of openfe (I couldn't get the recommended conda method to work, maybe that is just me).

The jobs start OK on the cluster, run for about a day, then die with the below error.

What is the problem? What file is not found? Where is the specified output? 'dG = None ± None' looks suspicious.

Any advice appreciated!

David

INFO:pymbar.mbar_solvers:Final gradient norm: 1.02e-08
INFO:pymbar.mbar_solvers:Reached a solution to within tolerance with adaptive
INFO:pymbar.mbar_solvers:Solution found within tolerance!
INFO:pymbar.mbar_solvers:Final gradient norm: 9.15e-09
INFO:pymbar.mbar_solvers:Reached a solution to within tolerance with adaptive
INFO:pymbar.mbar_solvers:Solution found within tolerance!
INFO:pymbar.mbar_solvers:Final gradient norm: 9.15e-09
INFO:pymbar.mbar_solvers:Reached a solution to within tolerance with adaptive
INFO:pymbar.mbar_solvers:Solution found within tolerance!
INFO:pymbar.mbar_solvers:Final gradient norm: 9.14e-09
Done with all simulations! Analyzing the results....
Here is the result:
dG = None ± None

Error: The protocol unit 'lig_ejm_31 to lig_ejm_46 repeat 0 generation 0' failed with the error message:
FileNotFoundError: 2

Details provided in output.

[IAlibay]

Hi @dkchalmers - apologies for the very very late response to this question.

Is this still an active issue? I suspect the FileNotFoundError is actually a bug from an old version of OpenFE. What version did you have installed?

[dkchalmers]

Hi Irfan,

Thanks for the reply. I managed to work around this by installing the development version. I don't know what version that was.

David

[IAlibay]

Ok great, I'll mark this thread as completed. Do let us know if you stumble upon any other issues.