My LigPrep job failed part way through. Is there any way that I can run the rest of the job?
Yes, you can restart distributed LigPrep jobs, from the command line.
- If you started the job from the command line with the -LOCAL option, you can rerun the job with the -RESTART option added to the command.
- If you did not start the job with -LOCAL, you can restart the subjobs that failed or did not run by specifying them with the -j option. For details, see Section 2.3 of the LigPrep User Manual.
If you are running LigPrep as a single job, there is no automated restart mechanism, but there are facilities for running a job from a particular stage or for running an individual stage from the command line.
- You can restart a LigPrep job from a given stage with the -run_from option. The entire stage that you start from is re-run, so any existing results from that stage are discarded. The job then continues on to the following stages.
- You can run individual job stages from the command line by using the -R option. The entire stage is re-run, so any existing results from that stage are discarded.
For information on the syntax of the -run_from and the -R option, run the ligprep command with the -h option.