[MMTK] Energy minimization of amidated peptide

Sabine Reisser sabine.reisser at kit.edu
Thu Jan 3 17:15:43 UTC 2013


I'm trying to energy minimize a 14 residue helical peptide with the last 
residue being an amide group.

My code is

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('protein.pdb')

minimizer = ConjugateGradientMinimizer(universe,
minimizer(convergence = 1.e-4, steps = 100)

When I run this, I get the Error:
   File "/usr/lib64/python2.7/site-packages/MMTK/ChemicalObjects.py", 
line 59, in __getattr__
     return getattr(self.type, attr)
AttributeError: 'AtomType' object has no attribute 'amber_atom_type'

When I just remove the amide group from the pdb file, minimization runs 
fine. How can I tell MMTK what the NHE group is?

Thanks for reading and cheers


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