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.
- Copy the
jobname.infile to a new job name, e.g.
jobname_resume.in. If there is a
jobname.featfile, copy that to
jobname_resume.in, and add the line
where N is the first ligand you want to dock in the new job. Look at the
jobname.logfile (shown in the Monitor panel in Maestro) to determine the last ligand docked successfully in the original job.
- Run the new job from the command line
$SCHRODINGER/glide [options] jobname_resume.in
- 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.maegzin the file names in this step and the next step, instead of
- Once the new job has completed, combine the results of the interrupted job with those of the new, resumed job using
$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.
#589: Is there any way to stop or kill a 'Stranded' Glide docking run but still recover any docking results and scores that...
#656: I started a job to screen a million molecules, and it failed before finishing. How can I recover my results and finis...
#1054: How can I restart a Glide docking calculation for which some subjobs failed?
#1589: I submitted a Glide docking job to our cluster a couple of weeks ago and we just had a system failure that caused our...
Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles