File: minimization.py

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clearAll()
pdb = PDBFile(Path().find("structures/bpti.pdb"))
S = System()
pdb.read(S)
getMainControl().insert(S)
getMolecularStructure().addHydrogens()
getMolecularControl().applySelector("element(H)")
amber = getMolecularStructure().getAmberFF()
amber.setup(S)
m = SteepestDescentMinimizer(amber)
m.minimize(100)