[MMTK] a question about DNA and the Amber forcefield in MMTK

Kristina Woods kristina.woods at gmail.com
Tue Sep 13 22:49:15 CEST 2005


Hi there,

I am trying to do a normal mode analysis of a fragment of DNA surrounded by 
a 3.5 angstrom layer of solvent (water + sodium ions) using the Amber 
forcefield. The DNA is imported from a .pdb file. When I attempt to do the 
minimization step of the normal mode analysis I get an error message that I 
believe means that I need to define something...but I am not sure what that 
something is. Here is the output from the minimization step:

------------------------------------------------------------------------------------------------------------------------

Python 2.2.2 (#1, Sep 24 2004, 16:10:19) 
[GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-5)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from MMTK import *
>>> from MMTK.ForceFields import Amber94ForceField
>>> from MMTK.NormalModes import NormalModes
>>> from MMTK.Minimization import ConjugateGradientMinimizer
>>> from MMTK.PDB import PDBConfiguration
>>> from MMTK.Trajectory import StandardLogOutput
>>> universe = InfiniteUniverse(Amber94ForceField())
>>> DNAconfiguration = PDBConfiguration('testna.pdb')
>>> universe.addObject(DNAconfiguration.createAll(None,1))
>>> minimizer = ConjugateGradientMinimizer(universe,
... actions=[StandardLogOutput(50)])
>>> minimizer(convergence = 1.e-4, steps = 50000)
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File 
"/usr0/user/kwoods/nmoldyn/lib/python2.2/site-packages/MMTK/Minimization.py", 
line 194, in __call__
evaluator = self.universe.energyEvaluator(threads=nt).CEvaluator()
File 
"/usr0/user/kwoods/nmoldyn/lib/python2.2/site-packages/MMTK/Universe.py", 
line 615, in energyEvaluator
threads, mpi_communicator)
File 
"/usr0/user/kwoods/nmoldyn/lib/python2.2/site-packages/MMTK/ForceFields/ForceField.py",
line 183, in __init__
self.global_data)
File 
"/usr0/user/kwoods/nmoldyn/lib/python2.2/site-packages/MMTK/ForceFields/MMForceField.py",
line 317, in evaluatorTerms
self.collectAtomTypesAndIndices(universe, global_data)
File 
"/usr0/user/kwoods/nmoldyn/lib/python2.2/site-packages/MMTK/ForceFields/MMForceField.py",
line 48, in collectAtomTypesAndIndices
type[a] = o.getAtomProperty(a, self.dataset
File 
"/usr0/user/kwoods/nmoldyn/lib/python2.2/site-packages/MMTK/ChemicalObjects.py",
line 326, in getAtomProperty
return levels[-1].getAtomProperty(atom, property, levels[:-1])
File 
"/usr0/user/kwoods/nmoldyn/lib/python2.2/site-packages/MMTK/ChemicalObjects.py",
line 628, in getAtomProperty
return getattr(self, property)
File 
"/usr0/user/kwoods/nmoldyn/lib/python2.2/site-packages/MMTK/ChemicalObjects.py",
line 54, in __getattr__
return getattr(self.type, attr)
AttributeError: AtomType instance has no attribute 'amber_atom_type'
>>> 

--------------------------------------------------------------------------------------------------------------------------------

Could anyone possibly tell me what I am doing wrong or what I need to 
define? 

Any help would definitely be appreciated!

Thanks,

Kristina :)
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