[Chimera-users] Problem loading trajectories ....

sharada sharada at ccmb.res.in
Mon Jan 22 21:58:54 PST 2007

Dear Chimera-users,
    Hello, I am a brand new entry into this forum. I  have started using chimera recently. I use Gromacs for my molecular modeling work.  Till I become friendly with chimera I need your valuable suggestions and cooperations. I  request you to kindly  bear with my very silly doubts and questions. Let me explain my problem.
    I have a protein of 35 residues and have simulated in a box of water for 10ns. My protein has charge so in order to neutralize it I have added counterions randomly placed them in the solvent(water). The  counter ions that I am adding are Cl- ions. I have created a *.trr file of the tracjectory for this 10ns. I would like to visulaize this trajectory using chimera. I am using Tools /MD/Ensemble Analysis /MD Movie to load the trr file. when I do so I am getting the following error:
Unknown molecule type: CL-
TypeError: __len__() should return an int
(see reply log for Python traceback info)
Traceback (most recent call last):
  File "/usr/local/chimera/share/__main__.py", line 59, in ?
    value = chimeraInit.init(sys.argv)
  File "CHIMERA/share/chimeraInit.py", line 318, in init
  File "CHIMERA/share/chimera/tkgui.py", line 2675, in eventLoop
  File "CHIMERA/lib/python2.4/lib-tk/Tkinter.py", line 965, in mainloop
  File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__
  File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror
  File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror
  File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__
  File "CHIMERA/share/chimera/baseDialog.py", line 231, in <lambda>
  File "CHIMERA/share/chimera/baseDialog.py", line 473, in OK
  File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 87, in Apply
  File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble
  File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble
  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 30, in __init__
  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 218, in __init__
  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 229, in _readHeader
  File "CHIMERA/lib/python2.4/xdrlib.py", line 194, in unpack_fstring
    if j > len(self.__buf):
TypeError: __len__() should return an int
What exactly is the problem ? How to solve it ?
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