[MMTK] a few questions about normal mode calc

OMAR NABEEL ALY DEMERDASH ondemerdash at wisc.edu
Wed Jul 13 03:34:19 CEST 2005

I am an MMTK beginner, so forgive me if my questions have obvious 

1.)  When I try to run the attached script, I get the following error 

Traceback (most recent call last):
  File "<input>", line 1, in ?
  File "/Users/omar/Desktop/fastnm_write_pdb2.py", line 13, in ?
    from MMTK.ForceFields import DeformationForceField
  File "/Library/Frameworks/Python.framework/Versions/2.4/lib/
python2.4/site-packages/MMTK/ForceFields/__init__.py", line 23, in ?
IOError: [Errno 13] Permission denied: '/Library/Frameworks/

There appears to be a problem opening up the DeformationForce Field 
module.  Does someone know what Errno 13 means? Is there a problem with 
read, write, execute permissions for that module?

2.)  What would be the simplest way to write the eigenvectors to 
individual files?

3.)  On page 114 of the MMTK instruction manual, it states that since 
the normal mode vectors are not mass-weighted, they are not orthogonal 
to each other.  Aren't the eigenvectors of a symmetric matrix such as 
the Hessian always orthogonal in a Cartesian basis?

Help is greatly appreciated!

Omar Demerdash

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