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Article ID: 1096 - Last Modified:

My LigPrep job failed part way through. Is there any way that I can run the rest of the job?

As of Suite 2011, you can restart distributed LigPrep jobs. 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 Suite 2010, you can restart a LigPrep job from a given stage with the -run_from option, from the command line. 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 in the current and earlier releases by using the -R option. The entire stage is re-run, so any existing results from that stage are discarded.

Thus, if you are running on a single processor with Suite 2010 or later, you can restart the job by using the ligprep command with the -run_from option.

If you are running Suite 2010 or earlier, and you have distributed the job over multiple processors, para_ligprep splits the ligands into batches, each of which is run as a single ligprep subjob. If the job fails, the subjobs will not necessarily all be at the same stage. To restart such a job, one option is to run each subjob by hand from the stage at which it failed. Another option is to collect the results of each subjob that completed a particular stage into a Maestro file. You would have one file for each completed stage from the original job. Then for each file, you can run para_ligprep -run_from and specify the stage that failed as the stage to run from. For earlier releases you would have to run each uncompleted stage separately with para_ligprep -R.

For information on the syntax of the -run_from and the -R option, see the LigPrep User Manual.

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