Helpful hints for using the MMTSB toolset in projects

This page contains a pot pourri of suggestions, hints and strategies that MMTSB developers have found helpful as they use these tools in their own research.

Good bookkeeping.
Especially when you're preparing a protein for those first simulations, it can be helpful to write the MMTSB commands and options that you use in a README file. Cut and paste from this README file onto the command line as you go. Several months from now when you are writing up your results or trying to prepare a new system, this will file will be invaluable.

If you want to join several commands together (say use convpdb.pl to select a given chain, followed by complete.pl to add hydrogen atoms, followed by another convpdb.pl to solvate the system), test out the first command then pipe it together with the next command. Test that series and then add the next command. By incrementally testing and piping these commands together in your README file, you'll ensure that you have the system prepared correctly and you'll have a shortcut for preparing other systems down the road.

Leveraging MMTSB scripts to obtain CHARMM input files.
Use the -cmd option that is available in many of the MMTSB commands to generate the corresponding CHARMM input file. This file can be further modified with other CHARMM commands and then run directly on the command line:
$CHARMMEXEC < inputfile > outputfile &