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
Dear Dave, When reporting a problem it is best to say what version of Chimera and what type of computer you are using. You can use "Help... Report a Bug" from the Chimera menu which will automatically include this information in what it sends to us. However, it is not necessary in this case since I believe the problem has been fixed. I tried your files in both 1.3 (latest production release, Dec 2008) and the current daily build. The production release gave the error, but in the daily build, MD Movie read the files successfully. Probably there were some cases that were not handled in the earlier version that have now been fixed. Daily builds: <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html> I recommend keeping your production release in addition to one or more daily builds... just give them different names or put them in different places. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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
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
participants (3)
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Dave Hassan -
Elaine Meng -
Eric Pettersen