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 re-saves the system for later use:

# . Set up a MM model.

mmModel = MMModelOPLS.WithParameterSet ( "protein" )

# . Get the system.

system = Unpickle ( "step3.pkl" )

system.Summary ( )

# . Add the energy model.

system.DefineMMModel ( mmModel )

system.Summary ( )

# . Save the system.

Pickle ( "step4.pkl", system )

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.