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How do I run LigPrep from the command line?

You can run LigPrep from the command line with the command $SCHRODINGER/ligprep, either for single processor or multiprocessor execution. (Prior to Suite 2011, you must use $SCHRODINGER/utilities/para_ligprep for multiprocessor execution).

LigPrep can be run with either a command input file that lists the options to be used, or from the command line by using options to modify the default behavior. The default behavior is discussed in Section 3.2.1 of the LigPrep User Manual. The options are listed in Section 2.2 by stage and category, and also in a Quick Reference sheet. The input file is described in Section 2.4

An efficient method to gather all of the LigPrep command options that you need for most types of jobs is to set up and run a small sample job from Maestro. LigPrep echoes the command that it uses in the log file, jobname.log. You can then copy and paste the options listed for the command line submission. Some examples of LigPrep job submission can be found in Section 3.2 of the manual.

If you want to distribute the LigPrep job across multiple processors, you can do so with the ligprep command (or with para_ligprep prior to Suite 2011). Distributed computing is described in Section 2.3 of the LigPrep User Manual, with examples. The command options to para_ligprep for the tasks are the same as for ligprep. You can specify the number of subjobs to run with the -NJOBS m option, and the number of processors with -HOST hostname:nproc.

Related Articles:

#88: Can I run a ligand preparation on multiple processors?
#1443: I would like to prepare a large ligand library using LigPrep. How should I proceed?

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