[MMTK] PDB file

Shirley Hui shirleyhui at alumni.uwaterloo.ca
Tue May 11 01:51:48 CEST 2004

I am trying to read in a PDB fille.
My code looks like this:
from MMTK import *
from MMTK.PDB import PDBConfiguration
from MMTK.ForceFields import Amber94ForceField
import sys

conf = PDBConfiguration('alanin.pdb')
chains = conf.createPeptideChains()
universe = InfiniteUniverse(Amber94ForceField())
print universe.energy()
print universe.energyTerms()['electrostatic']

When I try and specify the PDB file to be something that was not included in the source distribution (i.e. a configuration that is not 2YCC.pdb, insulin.pdb etc), I get errors.  For example, I got alanin.pdb from the protein databank.  I put this file in C:\Python23\Lib\site-packages\MMTK\Database\PDB.  When I run the code as above, I get the following error:

Traceback (most recent call last):
  File "C:\PYTHON23\lib\site-packages\Pythonwin\pywin\framework\scriptutils.py", line 310, in RunScript
    exec codeObject in __main__.__dict__
  File "C:\Python23\Scripts\shirl.py", line 6, in ?
  File "c:\python23\Lib\site-packages\MMTK\PDB.py", line 147, in __init__
    Scientific.IO.PDB.Structure.__init__(self, filename)
  File "C:\PYTHON23\Lib\site-packages\Scientific\IO\PDB.py", line 890, in __init__
  File "C:\PYTHON23\Lib\site-packages\Scientific\IO\PDB.py", line 1041, in parseFile
    type, data = file.readLine()
  File "C:\PYTHON23\Lib\site-packages\Scientific\IO\PDB.py", line 152, in readLine
    data = {'serial_number': line[1],
  File "C:\PYTHON23\Lib\site-packages\Scientific\IO\FortranFormat.py", line 122, in __getitem__
    return self.data[i]
IndexError: list index out of range

If instead I have insulin.pdb instead of alanin.pdb, it works.

Is there something I am doing wrong?  I even created an evironment variable in my PATH called MMTKPATH according to this link:  http://starship.python.net/crew/hinsen/mmtk_manual/database.html

I tried setting this env variable to be: C:\Python23\Lib\site-packages\MMTK\Database\PDB and C:\Python23\Lib\site-packages\MMTK\Database, but neither work??

Thanks in advance,

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