from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber99ForceField
from MMTK.Minimization import ConjugateGradientMinimizer
from MMTK.Trajectory import StandardLogOutput
from MMTK.NormalModes import VibrationalModes

universe = InfiniteUniverse(Amber99ForceField())
molecule = Protein('minimized.pdb')
universe.addObject(molecule)

modes = load('k2.modes')