This document is designed to help you set up an OpenFF QM benchmark using your own set of molecules.

If you experience any issues during any stage of the procedure please raise all issues here. You can also receive support on the Open Force Field Slack channel benchmarks-partners NOTE: all discussions are public so please do not disclose any molecule information you wish to remain private.

Installation

To keep things simple conda environments have been created which are fully self-consistent and contain at a minimum all of the required dependencies to run the calculations and generate the final analysis.

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• Where is the local QCArchive database stored

  • you can find the database in a path like ~/.qca/qcfractal/ on the machine where you activated the server.

• Why do I see stereochemistry issues in the initial step in the workflow?

  • All file reading and writing is done via the Open Force Field Toolkit which is , with many cheminformatics operations powered by RDKit. When we read in a molecule we check according to RDKits definitions with RDKit if the molecule has any missing stereochemistry information. We recommend using 3D SDF files where possible so that all stereochemistry is fully defined.

• Missing molecules?

  • During the workflow, multiple things can go wrong manly involving undefined stereochemistry when this happens a warning is shown about the molecule is moved to an error directory to keep track of.

  • During the analysis, you may notice some molecules are missing or the number of conformers of the molecule is not as expected. During optimization, we sometimes see proton transfer and the resulting optimized geometry is actually a tautomer of the input, in . In this case, the optimization is excluded from the analysis. This should not affect the results.

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