[Chimera-users] GROMACS trajectory

[Dave Hassan]

Hi All,

I'm trying to generate an MD move from a gromacs trajectory. I used
tools > MD/Ensemble Analysis > MD movie in the toolbar. I then get the
following error message:

VERSION 4.0.5
using floats
version 58  generation 17
9975 atoms
DICKERSON DODECAMER in water
17 atoms
456 residues
<type 'exceptions.IndexError'> Exception in Tk callback
  Function: <function command at 0x10ecc870> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/Applications/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py",
line 244, in command
    getattr(s, buttonFuncName(txt))()
  File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py",
line 458, in OK
    self.Apply()
  File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/EnsembleLoader.py",
line 92, in Apply
    self.callback)
  File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/__init__.py",
line 56, in loadEnsemble
    startFrame, endFrame, callback)
  File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/__init__.py",
line 67, in loadEnsemble
    ensemble = Gromacs(topology, trajectory, startFrame, endFrame)
  File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py",
line 25, in __init__
    self.topology = TprTopology(topology)
  File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py",
line 68, in __init__
    self._readTopology(version)
  File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py",
line 181, in _readTopology
    for i in range(numResidues)]
<type 'exceptions.IndexError'>: list index out of range

attached are the .trr and .tpr I used.

Any help would be greatly appreciated.

Thanks,
Dave Hassan
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Dickerson_grompp2em.tpr
Type: application/octet-stream
Size: 342060 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090628/52dd5c91/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Dickerson_md_em.trr
Type: application/octet-stream
Size: 7189200 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090628/52dd5c91/attachment-0001.obj>