MMTSB Tool Set Tutorial

This is the tutorial for the MMTSB Tool Set. Its purpose is to introduce the MMTSB tools in the context of typical applications and give more background information than what is available in the manual pages meant for quick reference.

The tutorial is sectioned into mostly independent parts and can be navigated through the sidebar on the left. It is not necessary to work through the whole tutorial to learn about one area of applications. However, when reading multiple sections it is recommended to follow the given order.


Tool Set Installation

Before continuing with the tutorial please check whether the MMTSB Tool Set and CHARMM are installed and setup properly so that the examples can be run succesfully. The Tool Set is available for download from this web site. If CHARMM is not available on your system it may be obtained from here.

To test whether the MMTSB Tool Set is correctly installed type in a shell window: 

aarex.pl -help
If this does not print out usage information for aarex.pl ensure that
  • the latest version is installed from the package available here,
  • the environment variable MMTSBDIR contains the name of the main directory of the installed MMTSB Tool Set, and that
  • the UNIX search path includes the MMTSB binary and perl directories
For further details please consult the installation instructions that come with the package or send email to mmtsb@scripps.edu.

In order for CHARMM to work with the MMTSB Tool Set a CHARMM executable for version c28a4, c29b1 or newer needs to be available and the environment variable CHARMMEXEC needs to to point to its location. Another variable CHARMMDATA is expected to point to a directory containing CHARMM parameter and topology files.

The variables may be checked with 

echo $CHARMMEXEC
echo $CHARMMDATA
and, if necessary, set with 
setenv CHARMMEXEC <full-path-of-CHARMM>
Running examples

The tutorial contains many examples that should be tried out while reading the tutorial. Most of the examples use input files from the directory $MMTSBDIR/bench/common-data that are available for download as a separate package.

It would be a good idea to copy all files from this directory into a new directory and run all examples out of this directory. This will leave the original package intact and provide room for experimenting with the MMTSB Tool Set.

All examples are designed to complete within seconds or minutes depending on the application and should not require large amounts of memory or disk space. Some examples that demonstrate parallel processing require adequate (parallel) hardware.