<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Dave,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Gromacs 4 trajectories are currently only supported in the daily build.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div><br></div><div>--Eric<br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Jun 28, 2009, at 7:11 PM, Dave Hassan wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi All,<br><br>I'm trying to generate an MD move from a gromacs trajectory. I used<br>tools > MD/Ensemble Analysis > MD movie in the toolbar. I then get the<br>following error message:<br><br>VERSION 4.0.5<br>using floats<br>version 58 generation 17<br>9975 atoms<br>DICKERSON DODECAMER in water<br>17 atoms<br>456 residues<br><type 'exceptions.IndexError'> Exception in Tk callback<br> Function: <function command at 0x10ecc870> (type: <type 'function'>)<br> Args: ()<br>Traceback (innermost last):<br> File "/Applications/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",<br>line 1747, in __call__<br> return apply(self.func, args)<br> File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py",<br>line 244, in command<br> getattr(s, buttonFuncName(txt))()<br> File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py",<br>line 458, in OK<br> self.Apply()<br> File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/EnsembleLoader.py",<br>line 92, in Apply<br> self.callback)<br> File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/__init__.py",<br>line 56, in loadEnsemble<br> startFrame, endFrame, callback)<br> File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/__init__.py",<br>line 67, in loadEnsemble<br> ensemble = Gromacs(topology, trajectory, startFrame, endFrame)<br> File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py",<br>line 25, in __init__<br> self.topology = TprTopology(topology)<br> File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py",<br>line 68, in __init__<br> self._readTopology(version)<br> File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/formats/Gromacs/Gromacs.py",<br>line 181, in _readTopology<br> for i in range(numResidues)]<br><type 'exceptions.IndexError'>: list index out of range<br><br>attached are the .trr and .tpr I used.<br><br>Any help would be greatly appreciated.<br><br>Thanks,<br>Dave Hassan<br><span><Dickerson_grompp2em.tpr></span><span><Dickerson_md_em.trr></span>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>