PURPOSE: A modified version of the standard In Situ Ligand Minimization.

This protocol adds several properties to the output .sd file including:

• -In-Situ Start Energy: The negative of the ligand energy (kcal/mol) before minimization.
• -In-Situ Final Energy: The negative of the final ligand energy (kcal/mol) after minimization.
• -In-Situ Final VDW: The negative of the final vdw energy of the ligand (kcal/mol) after minimization.
• -In-Situ Final Electrostatic: The negative of the final electrostatic energy of the ligand (kcal/mol) after minimization.

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

In Situ Ligand Minimization with VDW and Electro energies.xml file and enter it as the File Name.

REQUIREMENTS: Discovery Studio Embedded Collection. In order make use of all steps listed above, this protocol requires CHARMm or CHARMm Lite licenses

DISCLAIMER: This custom protocol is compatible with Discovery Studio 3.5 and Pipeline Pilot server version 8.5 CU3. 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.