[MMTK] Problem with Energy and Gradients Calculation

vanitha at cs.wisc.edu vanitha at cs.wisc.edu
Sun Nov 27 14:18:17 CET 2005

I again get Nan for another protein 1FSS.pdb. I'm confident that there are
no missing atoms in this protein. I have applied the Conjugate Gradient
Minimizer to this successfully in the past!
Just wondering if any of you would be willing to try this out for me... I
can email the PDB after I hear back from one of you.
I need to quickly figure out if it is the protein or something else that
is going wrong. Alternatively, can one of you point me to a protein for
which you are able to get an energy number using the following code? I can
then test my code for that protein to see if the problem recurs.

Here is the code (from Konrad Hinsen):

from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber94ForceField

universe = InfiniteUniverse(Amber94ForceField())
universe.protein = Protein('1FSS.pdb')

energy, gradients = universe.energyAndGradients()

print energy
print gradients.norm()

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