[Chimera-users] GROMACS trajectory

[Eric Pettersen]

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 at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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