ADL: Error in ADT

Reiner Villavicencio cyberworm_upm at yahoo.com
Sat Jan 21 20:05:35 PST 2006


Dear all,
   
       I have used the hin2pdbq.py script to convert my hyperchem LIGAND files so I can use them for Autodock. The convertion was successful including bonding info (conect) and I was able to load in in the ADT window. However when the program tries to interact with the molecule, error messages appear like as follows:
   
  Python 2.3.2 (#6, Dec 11 2003, 15:11:30) [GCC 2.95.3 20010315 (SuSE)] on linux2
Type "copyright", "credits" or "license()" for more information.
****************************************************************    
Personal firewall software may warn about the connection IDLE
makes to its subprocess using this computer's internal loopback 
interface.  This connection is not visible on any external
interface and no data is sent to or received from the Internet.    
****************************************************************    
IDLE 1.0      ==== No Subprocess ====
>>> ERROR ************************************************
Traceback (most recent call last):
File "/home/rv/mglTools/share/lib/python2.3/site-packages/ViewerFramework/VF.py", line 582, in tryto
result = apply( command, args, kw ) File "/home/rv/mglTools/share/lib/python2.3/site-packages/Pmv/bondsCommands.py", line 104, in doit    mol.buildBondsByDistance() File "/home/rv/mglTools/share/lib/python2.3/site-packages/MolKit/protein.py", line 398, in buildBondsByDistance
c.buildBondsBhtree()
File "/home/rv/mglTools/share/lib/python2.3/site-packages/MolKit/molecule.py", line 1038, in buildBondsBhtree
atoms = self.findType(Atom)
File "/home/rv/mglTools/share/lib/python2.3/site-packages/MolKit/protein.py", line 51, in findType
result = n.findType(_type, uniq=uniq)
File "/home/rv/mglTools/share/lib/python2.3/site-packages/MolKit/tree.py", line 204, in findType
raise RuntimeError ("could not find level of type %s"%what)
RuntimeError: could not find level of type MolKit.molecule.Atom
ERROR ************************************************
Traceback (most recent call last):
File "/home/rv/mglTools/share/lib/python2.3/site-packages/ViewerFramework/VF.py", line 582, in tryto
result = apply( command, args, kw )
File "/home/rv/mglTools/share/lib/python2.3/site-packages/AutoDockTools/autotorsCommands.py", line 431, in doit
mol.buildBondsByDistance()
File "/home/rv/mglTools/share/lib/python2.3/site-packages/MolKit/protein.py", line 398, in buildBondsByDistance
c.buildBondsBhtree()
File "/home/rv/mglTools/share/lib/python2.3/site-packages/MolKit/molecule.py", line 1038, in buildBondsBhtree
atoms = self.findType(Atom)
File "/home/rv/mglTools/share/lib/python2.3/site-packages/MolKit/protein.py", line 51, in findType
result = n.findType(_type, uniq=uniq)
File "/home/rv/mglTools/share/lib/python2.3/site-packages/MolKit/tree.py", line 204, in findType
raise RuntimeError ("could not find level of type %s"%what)
RuntimeError: could not find level of type MolKit.molecule.Atom

  What could be the problem?
  Thank you and good day.
   
    Reiner Villavicencio
  BS Biochemistry
  Department of Physical Sciences and Mathematics
  College of Arts and Sciences 
  University of the Philippines, Manila


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