ADL: and scripts

Jordi jbvqob at
Tue Oct 23 04:37:50 PDT 2007


When I try to execute the script "" included in MGLTools 1.4.6 I get the following error:

  [jordi at sauron QUIMIOTECA]$ /usr/local/Programs/MGLTools/share/bin/pythonsh $MGL_UTILS/ -d xxx
  setting PYTHONHOME environment
  Traceback (most recent call last):
    File "/usr/local/Programs/MGLTools/MGLToolsPckgs/AutoDockTools/Utilities24/", line295, in ?
    File "/usr/local/Programs/MGLTools-1.4.6/MGLToolsPckgs/Updates/tested/AutoDockTools/", line 179, in make_clustering
      dist = self.get_distance(cluster[0], conf)
    File "/usr/local/Programs/MGLTools-1.4.6/MGLToolsPckgs/Updates/tested/AutoDockTools/", line 129, in _get_distance_default
      dist = a.getRMSD(b.getCoords())
    File "/usr/local/Programs/MGLTools-1.4.6/MGLToolsPckgs/Updates/tested/AutoDockTools/", line 91, in getRMSD
      rmsd = rmsd_calc.computeRMSD(self.getCoords())
    File "/usr/local/Programs/MGLTools-1.4.6/MGLToolsPckgs/Updates/tested/mglutil/math/", line 38, in computeRMSD
      raise ValueError("input vector length mismatch")
  ValueError: input vector length mismatch

Similarly, if I try the script, I get:

  [jordi at sauron QUIMIOTECA]$ pythonsh /usr/local/Programs/MGLTools/MGLToolsPckgs/AutoDockTools/Utilities24/ -d xxx
  setting PYTHONHOME environment
  Traceback (most recent call last):
  line 89, in ?
      lig_fn = ll[1]+".pdbqt"
  IndexError: list index out of range

Could somebody explain what does that mean and how to fix it? I would also appreciate some explanation about what the script is supposed to do. Thanks in advance for the help.


Jordi Bujons Vilas, Ph.D.
Staff Scientist
Dept. of Biological Organic Chemistry
Instituto de Investigaciones Químicas y Ambientales de Barcelona
Consejo Superior de Investigaciones Científicas

Address: Jordi Girona 18-24, 08034 Barcelona, Spain
Phone: 34 934006158
Fax: 34 932045904
Email: jbvqob at

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