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Schrodinger

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General Description

Schrodinger is a molecular modelling package used primarily for drug design. It consists of 25+ standalone analysis applications: 4 of the more popular ones are Jaguar, MacroModel, Prime, and Glide. Schrodinger's graphical front end is called Maestro. Many of the applications also have command-line interfaces. Schrodinger has its own job control mechanism for submitting jobs which runs on top of the Sun Grid Engine.

Basic Usage

The submission of a Schrodinger job is different from any other job submission. The reason being that Schrodinger uses its own job control mechanism.

The control of a job can be done in the following ways listed by order of preference:

  • with regular SGE command
qstat –u username (to list all your jobs)
qdel #job_id (to delete your job)
  • with the Maestro gui to control job from the menu Applications->Monitor_Jobs
    • from there users can check the status of their jobs in more details. They can kill any jobs also (it will kill jobs from SGE scheduler job list as well)
  • with the jobcontrol command line
jobcontrol -kill  opteron-0-46ba1f76 (in the following glide example) to kill it

jobcontrol -g to access a simple gui

Glide job

An example of Glide job submission script (requesting 12 sub-jobs):

#!/bin/csh

#$ -M netid@nd.edu       # Email address for job notification
#$ -m abe                # Send mail when job begins, ends and aborts
#$ -q long   # Specify queue
#$ -N gridprep       # Specify job name
#$ -pe smp 12

module load schrodinger  # Required modules


"${SCHRODINGER}/glide" input_file.in -WAIT  -OVERWRITE -HOST "localhost:12" -NJOBS 12 

Liaison job

To submit a Liaison job using Maestro, please refer to the documentation $SCHRODINGER/doc/liaison/user_manual.

At some point you will be see the following window: Liaison Image

If the job uses only NPROC=1 processor , select 'serial' in the host field instead of localhost.

If the job uses NPROC=8 processors, select 'mpi-8' in the pe field.

For a command-line submission, you can find more details at page 36 of the documentation. Use -HOST control job option as documented previously in the Glide job section.


For further information about Schrodinger suite (http://www.schrodinger.com/), please refer to the documentations located in $SCHRODINGER/doc.

Useful Options

  • jobcontrol -list - shows jobs submitted using Schrodinger's job scheduler.
  • jobcontrol -recover <jobID> - will attempt to gracefully terminate jobs listed as stranded by the job scheduler, and release the Schrodinger license.
  • jobcontrol -kill <jobId> - will attempt to gracefully terminate jobs listed as running by the job scheduler. If the job is listed as stranded, try recovering it first (see above), then killing it.
  • jobcontrol -delete -force <jobid> - This command should only be used as a last resort, because it removes all job control information for the given job. However, if the job is actually alive, its job record may eventually reappear after using this command.
  • maestro -SGL - will run the program using software to render the models. May solve problem if program freezes/crashes repeatedly.

Note: to check the Schrodinger license status:

module load schrodinger
licutil -list -file  /opt/crc/schrodinger/2013u2/license

Further Information

See the official website: Schrodinger

The User Guides, v.2011u1, for Maestro, Prime and other tools may be found at:

/afs/crc.nd.edu/x86_64_linux/schrodinger/2011u1/docs