[MMTK] Errors in energy evaluation with mg ion

Ryan Gutenkunst rng7 at cornell.edu
Tue Jul 20 21:14:52 CEST 2004


Hi all,

I'm trying to simulate a protein along with a magnesium ion present in 
the pdb file, and I'm getting errors in the energy evaluation.

Below I've attached the traceback, and my Database files Atoms/mg and 
Molecules/mg

Does anyone know what's wrong?

Thanks for any help,

The traceback is here:

Traceback (most recent call last):
   File "run.py", line 78, in ?
     minimizer(convergence = 1.e-3, steps = minSteps)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/Minimization.py", 
line 124, in __call__
     mpi_communicator=comm)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/Universe.py", 
line 615, in energyEvaluator
     threads, mpi_communicator)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/ForceField.py", 
line 183, in __init__
     self.global_data)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/MMForceField.py", 
line 320, in evaluatorTerms
     global_data)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/ForceField.py", 
line 93, in evaluatorTerms
     global_data)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/MMForceField.py", 
line 301, in evaluatorTerms
     subset2, global_data)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/ForceField.py", 
line 93, in evaluatorTerms
     global_data)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/NonBondedInteractions.py", 
line 132, in evaluatorTerms
     eps, sigma, mix = self._ljParameters(t, global_data)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/MMForceField.py", 
line 68, in _ljParameters
     return self.dataset.ljParameters(type)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/Amber/AmberData.py", 
line 296, in ljParameters
     p = ljp.getEntry(name)
   File 
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/Amber/AmberData.py", 
line 426, in getEntry
     return self.entries[name]
KeyError: 'MG'

-- 
Ryan Gutenkunst               |
Cornell Dept. of Physics      |       "It is not the mountain
                               |        we conquer but ourselves."
Clark 535 / (607)255-6068     |        -- Sir Edmund Hillary
AIM: JepettoRNG               |
          http://www.physics.cornell.edu/~rgutenkunst/
-------------- next part --------------
name = 'MG'

MG = Atom('Mg')

pdbmap = [('MG', {'MG': MG})]

amber_atom_type = {MG: 'MG'}

amber_charge = {MG: 2}

configurations = {'default': Cartesian({MG: (0, 0, 0)})}
-------------- next part --------------
#info from http://www.webelements.com/webelements/elements/text/Mg/radii.html
name = 'magnesium'
symbol = 'Mg'

mass = [(23.9850423, 78.99), (24.9858374, 10.00), (25.9825937, 11.01)]

color = 'gray'

vdW_radius = 0.173


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