Hermes 2023.1 or 2023.2 may fail to run the ligand overlay tool with the following error:
MoleculeGeometryPreferences: there was a problem initialising Mogul: errors=Problem reading initialisation file
This issue is resolved in the 2023.3 release.
To enable this to work with 2023.1 or 2023.2 releases, a workaround is to set CCDC_MOGUL_INITIALISATION_FILE to the mogul.ini file in your Hermes installation, e.g.
export CCDC_MOGUL_INITIALISATION_FILE=/home/user/CCDC/ccdc-software/hermes/bin/mogul.ini
before starting Hermes.
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