[MMTK] Segmentation fault, normal modes calculation

Lars Skjærven larsss at gmail.com
Fri Jan 5 11:23:11 CET 2007

I am trying to calculate the normal modes of a large chaperon (GroEL/ 
GroES complex, pdb code: 2cgt/1aon/1xck/2eu1). We know that these pdb- 
files have some missing residues, which we think may cause the  
problem. I have tried different methods, but they all return the same  
error. Namely "Segmentation fault". No other details are written to  
the screen. Running throught the gdb we found that it crashes at line  
668 in MMTK_forcefield.c. This happens both om x86 and AMD 64 system.

Any suggestions?

Lars Skjærven

Python code as copied for the MMTK home-page:
from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import DeformationForceField
from MMTK.FourierBasis import FourierBasis, estimateCutoff
from MMTK.NormalModes import NormalModes, SubspaceNormalModes
from MMTK.Visualization import view

# Construct system (protein is loaded from file)
universe = InfiniteUniverse(DeformationForceField())
universe.protein = Protein('2cgt.pdb', model='calpha')

# Find a reasonable basis set size and cutoff
nbasis = max(10, universe.numberOfAtoms()/5)
cutoff, nbasis = estimateCutoff(universe, nbasis)
print "Calculating %d low-frequency modes." % nbasis

if cutoff is None:
     # Do full normal mode calculation
     modes = NormalModes(universe)
     # Do subspace mode calculation with Fourier basis
     subspace = FourierBasis(universe, cutoff)
     modes = SubspaceNormalModes(universe, subspace)

save(modes, '2cgt.modes')

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