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Step 4

The program to generate a MM model is very simple. It recovers the system created in Step 3, applies an OPLS MM model (with the "protein" parameter set), and then resaves the system for later use:

# . Set up a MM model. mmModel = MMModelOPLS ( "protein" ) # . Get the system. system = Unpickle ( "../step3/step3.pkl" ) # . Add the energy model. system.DefineMMModel ( mmModel ) # . Save the system. mmModel.ClearModelBuildingData ( ) Pickle ( "step4.pkl", system )

The statement mmmodel.ClearModelBuildingData is unnecessary for the program to work but serves to reduce the size of the file step4.pkl by eliminating irrelevant model-building data from the instance variable mmModel.

This step will fail if there are definitions or parameters missing from the OPLS parameter set. Generation of force field parameters is a complex topic in its own right and will not be covered in this tutorial. However, the Force Fields tutorial describes how to create a parameter set or to augment an existing one if the appropriate definitions are at hand.