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The input path must be the output path of step 1. The custom parameters path can be specified with the option --opls-dir, which defaults to ~/.schrodinger/opls_dir/. If the specified or the default --opls-dir does not exist, the directory will be created and initialized. This could be the case if you are a new user or you want to create a separate custom parameter directory.
Note: For Schrodinger 2021-1 and later, the above command won’t work in the current version (10/06/2021). The quick workaround is to run instead of the above command the standard Schrodinger command:
$SCHRODINGER/utilities/custom_params merge 7-schrodinger-ffb/ffb_openff_benchmark_oplsdir ~/.schrodinger/opls_dir
Afterwards you can continue the protocol with the next steps (3a or 3b, see below).
Step 3a: Run optimization without custom parameters
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The output files are very similar. They only contain one more column giving the name of the MM conformer which was matched to the reference (QM) conformer, i.e. which was closest based on the RMSD.
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6-2. Generate plots
The final openff-benchmark report plotscommand takes the directory containing the csv files as an input (either the output of compare-forcefieldsor match-minima).
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| Code Block |
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openff-benchmark report plots --input-path 5-compare_forcefields/ --ref-method b3lyp-d3bj |
And for match-minima:
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openff-benchmark report plots --input-path 5-match_minima/ --ref-method matched_b3lyp-d3bj |