OpenEye

Overview

A portfolio of molecular modeling applications for pharmaceutical research.

Restrictions on use

This software is licensed to a specific research group.

You may only use the software for pure non-commercial research in which the results of the research will be promptly released into the public domain.

You must be in the openeye unix group to use this software.

Set up procedure

Please load the module for the version you are interested in:

module load apps/binapps/openeye/v2015.jun.5
module load apps/binapps/openeye/v2012.jun.1

Running the application

Serial jobs

• Ensure you have the modulefile loaded
• Create a batch submission script, the example below uses omega2:

     
  #$ -V
  #$ -cwd
  
  omega2 -in 1_p0.0.mol2.gz -out test_p0.0.oeb.gz -prefix test_p0.0
  

• Submit: qsub scriptname

Parallel jobs

• Ensure you have the modulefile loaded
• Create a batch submission script, the example below uses omega2:

    
  #$ -V
  #$ -cwd
  #$ -pe openeye-smp.pe 4
  
  ### The next line works for omega2 in v2012.jun.1
  oempirun -hostfile machinefile.$JOB_ID -np $NSLOTS omega2 -in p0.0.mol2.gz -out p0.0.oeb.gz -prefix new_p0.0
  
  ### Use this line for omega2 in v2015.jun.5
  omega2 -mpi_np $NSLOTS -in $p0.0.mol2.oeb.gz -out $p0.0.mol2_CONF.oeb.gz -prefix p0.0.mol2
  
  

• Submit: qsub scriptname

Important notes about running openeye in parallel

• When submitting openeye jobs to the batch system, the openeye-smp.pe SGE parallel environment must be used; this ensures proper allocation of openeye processes to compute nodes.
• You must include -hostfile machinefile.$JOB_ID -np $NSLOTS otherwise the job will fail.
• It is not currently possible to run an openeye job on more than 12 cores.

Further info

• There are a large number of applications in this software – please see the openeye documentation.
• You can find out the version number of a particualar openeye application by typing in the command for that application without any parameters.
• Each openeye application has some text based help accessible from the command line. For example:

  brood --help

• openeye knowledgebase