PURPOSE: The attached protocol allows you to generate an energy map for a specific torsion in a molecule.

A typed molecule, in which there are 4 selected atoms defining a torsion, is chosen as the Input Typed Molecule. This structure is minimized with the 4 selected atoms fixed. The output from this first minimization is stored and the torsion angle is increased by the Torsion Angle Increment value. Again the structure is minimized with the torsion atoms fixed and the process is repeated until all the torsion values have been sampled and minimized.

The final minimized structure with each increment torsion has the extension "#_finalMin.dsv". All final minimized conformations are then combined into one dsv file called 'min_conformations.dsv'.

Note, if Minimization Max Steps is set to zero then no Minimization is performed and the energy is simply calculated for each torsion value conformation.

The charting tools in Discovery Studio can be used to plot the Torsion Angle vs. CHARMm Energy.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in Discovery Studio only, go to the Protocol Explorer, right-click over the folder you want to add the protocol to, choose Import, navigate to the location of the Torsion Forcing with Minimization.xml file and enter it as the File Name.

REQUIREMENTS: An Input Typed Molecule with 4 selected atoms. Discovery Studio Embedded Collection. DS CHARMm.

DISCLAIMER: This custom protocol is compatible with Discovery Studio 3.0/3.1 and Pipeline Pilot server version 8.0.1CU2/8.5.0.  It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.