This module is currently under development. Users are referred to the examples demonstrated on the documentation page for MMTSB Tools Set (see below). Also, the workshop tutorial materials, referenced on the main MMTSB page, provide additional examples of using this tool with CHARMM and Amber.

Within the MMTSB Tool Set energy minimization can be carried out with CHARMM or Amber through the utilities minCHARMM.pl and minAmber.pl that provide interfaces to either modeling package. Within CHARMM, Amber and OPLS force fields can be used in addition to standard CHARMM force fields. These tools, as all the other tools for force-field based all-atom modeling, require that recent versions of CHARMM (c30b1 or newer) and/or Amber (7 or newer) are installed and error messages will result if the program packages are either missing or only older versions are available.

The perl tools minCHARMM.pl and minAmber.pl, as well as other tools for running energy evaluations and molecular dynamics, are meant to relieve the user from having to learn how to use the fairly complex molecular modeling packages directly if the applications consist of relatively simple routine tasks. The tool set then automatically takes care of all necessary setup tasks under a reasonable set of assumptions that should be appropriate for most standard applications. It is still possible, though, to control the energy terms and simulation parameters through an extensive set of options that can be specified to alter the default behavior, if necessary.