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Ryan-<br>
A quick look at your errors suggests that the energy evaluator is
looking for the Lennard-Jones parameters.&nbsp; I could be wrong, but check
out the argon entry in Database/Atoms/ar for comparison.&nbsp; <br>
Good luck.<br>
Eric<br>
<br>
Ryan Gutenkunst wrote:<br>
<blockquote type="cite" cite="mid40FD6F2C.5090607@cornell.edu">Hi all,
  <br>
  <br>
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.
  <br>
  <br>
Below I've attached the traceback, and my Database files Atoms/mg and
Molecules/mg
  <br>
  <br>
Does anyone know what's wrong?
  <br>
  <br>
Thanks for any help,
  <br>
  <br>
The traceback is here:
  <br>
  <br>
Traceback (most recent call last):
  <br>
&nbsp; File "run.py", line 78, in ?
  <br>
&nbsp;&nbsp;&nbsp; minimizer(convergence = 1.e-3, steps = minSteps)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/Minimization.py",
line 124, in __call__
  <br>
&nbsp;&nbsp;&nbsp; mpi_communicator=comm)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/Universe.py",
line 615, in energyEvaluator
  <br>
&nbsp;&nbsp;&nbsp; threads, mpi_communicator)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/ForceField.py",
line 183, in __init__
  <br>
&nbsp;&nbsp;&nbsp; self.global_data)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/MMForceField.py",
line 320, in evaluatorTerms
  <br>
&nbsp;&nbsp;&nbsp; global_data)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/ForceField.py",
line 93, in evaluatorTerms
  <br>
&nbsp;&nbsp;&nbsp; global_data)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/MMForceField.py",
line 301, in evaluatorTerms
  <br>
&nbsp;&nbsp;&nbsp; subset2, global_data)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/ForceField.py",
line 93, in evaluatorTerms
  <br>
&nbsp;&nbsp;&nbsp; global_data)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/NonBondedInteractions.py",
line 132, in evaluatorTerms
  <br>
&nbsp;&nbsp;&nbsp; eps, sigma, mix = self._ljParameters(t, global_data)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/MMForceField.py",
line 68, in _ljParameters
  <br>
&nbsp;&nbsp;&nbsp; return self.dataset.ljParameters(type)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/Amber/AmberData.py",
line 296, in ljParameters
  <br>
&nbsp;&nbsp;&nbsp; p = ljp.getEntry(name)
  <br>
&nbsp; File
"/afs/msc.cornell.edu/home/jsethna/ryang/installed/lib/python2.3/site-packages/MMTK/ForceFields/Amber/AmberData.py",
line 426, in getEntry
  <br>
&nbsp;&nbsp;&nbsp; return self.entries[name]
  <br>
KeyError: 'MG'
  <br>
  <br>
  <pre wrap="">
<hr width="90%" size="4">
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)})}
  </pre>
  <pre wrap="">
<hr width="90%" size="4">
#info from <a class="moz-txt-link-freetext" href="http://www.webelements.com/webelements/elements/text/Mg/radii.html">http://www.webelements.com/webelements/elements/text/Mg/radii.html</a>
name = 'magnesium'
symbol = 'Mg'

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

color = 'gray'

vdW_radius = 0.173
  </pre>
  <pre wrap="">
<hr width="90%" size="4">
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  </pre>
</blockquote>
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