[MMTK] Errors in energy evaluation with mg ion

Eric Zollars zollars at caltech.edu
Tue Jul 20 23:28:46 CEST 2004


Ryan-
    The last lines of the file ForceFields/Amber/amber_parm94 
(everything below the line MOD4   RE) are used in the vdW calculation.  
Konrad referenced all the values as well.  There does not currently 
appear to be a Mg.
Eric

Ryan Gutenkunst wrote:

> 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'
>
>------------------------------------------------------------------------
>
>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)})}
>  
>
>------------------------------------------------------------------------
>
>#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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