Hi Dave, Gromacs 4 trajectories are currently only supported in the daily build. I'd like to second Elaine's suggestion to send these kind of problem reports to chimera-bugs, particularly ones with large attachments like this. I see that you did send in such a report on Friday afternoon, so I guess I also counsel patience :-) since such a report may not get turned around until the following Monday. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 28, 2009, at 7:11 PM, Dave Hassan wrote:
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 < Dickerson_grompp2em .tpr
<Dickerson_md_em.trr>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users