Article ID: 656 - Last Modified: December 14, 2011
I started a job to screen a million molecules, and it stopped before finishing. How can I recover my results and finish the docking run?
First, note that a job with one million molecules is too large a job for a single Glide process. You should distribute such large screens by splitting the job into many subjobs, and if possible distribute it over multiple processors (these are options in the Start dialog box). Even if you use only a single processor, splitting the job into subjobs avoids problems with a single large job failing and makes it easier to restart. We suggest making the subjobs no larger than 50000 molecules.
To recover your existing results, copy the
jobname_raw.maegz file from the job's scratch directory, if it still exists, to a safe location. The scratch directory is
tmpdir is defined in your hosts file (
$SCHRODINGER/schrodinger.hosts by default) for the host entry you used for the job. If this file is not there, you will have to rerun the entire job.
If you recover the existing results, to finish the job, copy the original
jobname.in file to give it a new name, then add the keyword
LIGAND_START to the file with the new starting ligand number as its value. This should be the ligand that the original job failed on.
If your recovered
_raw.mae file contains more than 100K docked poses, you won't be able to sort it using
$SCHRODINGER/utilities/glide_sort; instead, you'll have to divide the file into subsets with
$SCHRODINGER/utilities/maesubset. Then combine these sorted subsets with the
_lib.mae file from the new job with
Keywords: large job , subjobs, recover raw file, scratch directory, LIGAND_START keyword, merging results
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