How can I restart a Glide docking calculation for which some subjobs failed?

First, you can set the environment variable SCHRODINGER_MAX_RETRIES, so that the glide command tries to re-run failed subjobs the number of times specified by this environment variable. If you still have failed subjobs when the job finishes, you can restart the job with $SCHRODINGER/glide -RESTART to run the failed subjobs. Of course you should check that the failures were not due to problems with the structures before rerunning the subjobs.

See Section 7.3.4 of the Glide User Manual for more information.

Keywords: Glide, subjobs, failure, restart

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