Openeye

Overview

A portfolio of molecular modelling 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/oe-suite

We now recommend that you do this in your batch job (rather than on the command line on the login node) as per the examples below.

Running the application

Versions of the components

All the main components of openeye are installed to the same ‘top level’ directory. Underneath this each component has it’s own directory and below that a directory for each version of that component. When a new version of a component is installed it will automatically become the default for that component. If the version you use is important to you then please always call a specific version of a component.

For example, omega2 has three versions installed 3.1.2.2, 3.1.0.3 and 3.0.1.2. By default 3.1.2.2 is the one that will be run when you use omega2 is 3.1.0.3. In order to avoid the installation of a new version changing the one you get use the following command:

omega2 -use_version 3.1.0.3

To find out what versions of a component are available you will need to look in the install. For example to check omega2:

ls -l $OPENEYEDIR/arch/redhat-RHEL7-x64/omega

Python Toolkit

The Openeye Python Toolkit v2010.10.1 is available at $OEROOT/oe-python3-2018.Oct.1

Anaconda python will be automatically loaded for you by the oe-suite modulefile and it also sets $PYTHONPATH.

Serial jobs

• Create a batch submission script, the example below uses omega2:

  #!/bin/bash --login
  #$ -cwd
  
  module load apps/binapps/openeye/oe-suite
  omega2 -use_version 3.1.0.3 -in 1_p0.0.mol2.gz -out test_p0.0.oeb.gz -prefix test_p0.0
  

• Submit: qsub scriptname

Parallel jobs

When submitting openeye jobs to the batch system, the smp.pe SGE parallel environment must be used; this ensures proper allocation of openeye processes to compute nodes.

• Create a batch submission script, the example below uses oeomega:

  #!/bin/bash --login
  #$ -cwd
  #$ -pe smp.pe 4
  module load apps/binapps/openeye/oe-suite
  
  oeomega -use_version 3.1.0.3 macrocycle -in pdb_10_examples.oeb -prefix pdbexamples -mpi_np $NSLOTS
  

• Submit: qsub scriptname

Further info

• There are a large number of applications in this software – please see the openeye documentation.
• Each openeye application has some text based help accessible from the command line. For example:

  omega2 -use_version 3.1.0.3 --help