[MMTK] Potential Energy: NaN issue

Reginald Smith rsmith at sloan.mit.edu
Sun Jan 27 23:47:42 UTC 2013

Hi, I was trying to test out the code for MMTK on an AWS Ubuntu EC2
instance with Python 2.7 installed. I got NetCDF, Scientific Python, and
MMTK loaded and then I created a test program to rapidly calculate the
minimum free energy of a short peptide sequence, AAAAA. However, that (and
any other sequence I tried) kept giving potential energy and gradient
results of not-a-number (NaN). Below is my code and any help is appreciated.

from MMTK import *
from MMTK.Proteins import PeptideChain
from MMTK.ForceFields import Amber94ForceField
from MMTK.NormalModes import NormalModes
from MMTK.Minimization import ConjugateGradientMinimizer
from MMTK.Trajectory import StandardLogOutput
from MMTK.Visualization import view

# Create one peptide and calculate energy
universe = InfiniteUniverse(Amber94ForceField())
universe.peptide = PeptideChain('AAAAA',n_terminus=0,c_terminus=0)
print universe.peptide.sequence()
print len(universe.peptide)
# Minimize
minimizer = ConjugateGradientMinimizer(universe,
minimizer(convergence = 1.e-3, steps = 10000)

Reginald Smith (史瑞吉)
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