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Can I run a ligand preparation on multiple processors?

Yes. You can do this when you start the LigPrep job from Maestro, in the Job Settings dialog box (or Start dialog box, prior to the 2013-1 release), or you can specify multiple processors from the command line with the ligprep command.

For multiprocessor submission, there are two choices to be made: the number of processors to use simultaneously (CPUs), and the number of subjobs to divide the ligands into (NJOBS). For load balancing, we suggest to choose at least three subjobs per processor. If the queue controlling the subjob submission is very full, perhaps one subjob per requested processor could be more appropriate. By default, the preparation is divided into subjobs of 10,000 structures each.

If you are processing a large number of structures, you may need to restart the job if there is some sort of failure. To allow restarting, you should use the -LOCAL option, which uses the job launch directory for all I/O. The launch directory should therefore be accessible on the host on which you run the job, e.g. as a network-mounted disk.

Here is an example of a command-line ligprep submission.

$SCHRODINGER/ligprep -LOCAL -NJOBS 20 -HOST big_host:5 options

The options are the normal LigPrep options. This multiprocessor preparation would be divided into 20 subjobs, and 5 processors would be used simultaneously on the host "big_host" until all 20 subjobs are completed. See the section "Distributing LigPrep Jobs" in the LigPrep User Manual for more information. If you need to restart the job, add -RESTART to the command and resubmit it, with the same options as the original submission.

Related Articles:

#1251: How do I run LigPrep from the command line?
#1443: I would like to prepare a large ligand library using LigPrep. How should I proceed?

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