MGLTools

Overview

MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures.

This version includes a self-contained version of Python 2.5.

Version 1.5.6 is installed on the CSF.

Restrictions on use

There are no restrictions on accessing these tools. However users must agree to cite the software packages in any publications in which work is presented from these packages. Please ensure you follow the requires at the MGLTool License Page.

Set up procedure

To access the software you must first load the modulefile:

module load apps/binapps/mgltools/1.5.6

Running the application

Please do not run MGLTools on the login node. Jobs should be submitted to the compute nodes via batch and any applications using a GUI should be submitted using qrsh to schedule an interactive session.

Start an Interactive Session

The simplest way to run the MGL Tools (such as AutoDockTools and other graphical tools) is to start an interactive session via qrsh and then run the MGL Tools. Use the following commands:

# On the CSF login node, start an interactive session on a backend node:
qrsh -l inter -l short
   #
   # Wait for a new prompt to appear
   # If you get an error message, try again later.

# Now on the backend node, set up to use MGL Tools:
module load apps/binapps/mgltools/1.5.6

You can now run the required MGLTools application on the backend node. For example

# Run the required tool - e.g., adt:
adt

To access the python 2.5 shell that comes with MGL Tools:

pythonsh

The above has the PYTHONPATH environment variable set to the following path:

/opt/gridware/apps/binapps/mgltools/1.5.6/MGLToolsPckgs

When finished with your interactive session you must exit from the backend node:

exit

# We are now back on the CSF login node

Further info

• MGLTools website

Updates

None.