[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
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
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!
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