def optimize(self):
"""Run the optimization with MMTK"""
print '\n-------------------------------------------------------------------------------'
print '\n MMTK Optimization starts...'
print '\t.. building universe'
configuration = PDBConfiguration(self.temp_pdb_file)
# Construct the nucleotide chain object. This also constructs positions
# for the missing hydrogens, using geometrical criteria.
chain = configuration.createNucleotideChains()[0]
universe = InfiniteUniverse()
universe.addObject(chain)
restraints = self.create_restraints(chain)
# define force field
print '\t.. setting up force field'
if restraints:
ff = Amber94ForceField() + restraints
else:
ff = Amber94ForceField()
universe.setForceField(ff)
# do the minimization
print '\t.. starting minimization with %i cycles'%self.cycles
minimizer = ConjugateGradientMinimizer(universe)
minimizer(steps = self.cycles)
# write the intermediate output
print '\t.. writing MMTK output to %s'% self.temp_pdb_file
if self.model_passive:
print '\t (please note that MMTK applies a different numeration of residues.\n\t The original one will be restored in the final output).'
universe.writeToFile(self.mmtk_output_file)
open(self.temp_pdb_file, 'w').write(open(self.mmtk_output_file).read())
print '\n-------------------------------------------------------------------------------'
# 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(f"{mode}")
# Show animation of the first non-trivial mode
view(modes[6])
def minimize(self, out_pdb="min.pdb"):
minimizer = ConjugateGradientMinimizer(self._universe)
minimizer(convergence=1.e-3, steps=10000)
self._write_pdb(out_pdb)
return None
def minimize_all_replicas(self, convergence=1.e-3, steps=2000):
for k, universe in enumerate(self._universes):
print("Minimizing relica", k)
minimizer = ConjugateGradientMinimizer(universe)
minimizer(convergence=convergence, steps=steps)
return None