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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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