Normal modes of a protein — MMTK User Guide 2.7.7 documentation

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# Normal modes of a protein

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    # Standard normal mode calculation.
    #

    from MMTK import *
    from MMTK.Proteins import Protein
    from MMTK.ForceFields import Amber94ForceField
    from MMTK.NormalModes import VibrationalModes
    from MMTK.Minimization import ConjugateGradientMinimizer
    from MMTK.Trajectory import StandardLogOutput
    from MMTK.Visualization import view

    # Construct system
    universe = InfiniteUniverse(Amber94ForceField())
    universe.protein = Protein('bala1')

    # Minimize
    minimizer = ConjugateGradientMinimizer(universe,
                                           actions=[StandardLogOutput(50)])
    minimizer(convergence = 1.e-3, steps = 10000)

    # Calculate normal modes
    modes = VibrationalModes(universe)

    # Print frequencies
    for mode in modes:
        print mode

    # Show animation of the first non-trivial mode
    view(modes[6])

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