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Article ID: 1634 - Last Modified: January 22, 2013

My serial Glide job was interrupted. Can I resume the job without losing the results of ligands already docked in the original job?

If you need to resume a serial Glide job in the middle, you'll have to run a new Glide job on the remaining ligands and then combine those results with the partial results of the original job.

  1. Copy the jobname.in file to a new job name, e.g. jobname_resume.in. If there is a jobname.feat file, copy that to jobname_resume.feat.
  2. Edit jobname_resume.in, and add the line

    LIGAND_START N

    where N is the first ligand you want to dock in the new job. Look at the jobname.log file (shown in the Monitor panel in Maestro) to determine the last ligand docked successfully in the original job.
  3. Run the new job from the command line

    $SCHRODINGER/glide [options] jobname_resume.in

  4. Sort the raw pose file from the original, interrupted job:

    $SCHRODINGER/utilities/glide_sort -o jobname_interrupted_pv.maegz jobname_raw.maegz

    If you have requested ligand-only results from your Glide job, use _lib.maegz in the file names in this step and the next step, instead of _pv.maegz.
  5. Once the new job has completed, combine the results of the interrupted job with those of the new, resumed job using glide_merge:

    $SCHRODINGER/utilities/glide_merge -o jobname_pv.maegz jobname_interrupted_pv.maegz jobname_resume_pv.maegz

    The file 'jobname_pv.maegz' is the final pose file with the complete docking results for all input ligands.

Instead of running a serial job on your entire ligand set, you can split the job into subjobs and run it as a distributed job (even if you only have one processor). Distributed Glide (and VSW) jobs can be restarted. When they restart, individual incomplete subjobs are rerun from the beginning, so you should make sure that the subjobs aren't too big. For example, if you are running a Glide XP job with several hundred ligands, you might want to split the job into subjobs with 20 or so ligands, so that the amount of work lost if the job fails is relatively small.

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