<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Gleb,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>If you are using Gromacs 5 trajectories, you have to be using at least version 1.10.2 of Chimera. If you are using that version (or later), please use “Report a Bug” in Chimera’s Help menu to file a bug report and attach your topology file to the bug report. Thanks!</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On May 13, 2016, at 1:46 AM, James Starlight <<a href="mailto:jmsstarlight@gmail.com" class="">jmsstarlight@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Chimera users!<br class=""><br class=""><br class="">I am in charge with the analysis of protein-protein association during<br class="">long molecular dynamic simulation where my system was parametrized<br class="">using MARTINI CG force field. In particularly I am interesting to<br class="">find residues on one of the protein which are crustal for the binding<br class="">interface established during this MD.<br class="">For that purpose I am trying to use Chimera to load trajectory and<br class="">corresponded tpr file using MD movie plugin and than to<br class="">map contact maps produced by Gromacs onto the 3D structure using Chimera.<br class="">The problem that Chimera does not recognize properly the trajectory<br class="">and topology. Briefly I have removed all solvent from both files<br class="">before loading them to the Chimera using editconf and gmx convert-tpr<br class="">obtaining eventually trajectory and topology with the same number of<br class="">atoms.<br class=""><br class=""><br class="">Than when I load it to Chimera that is the error which MD movie sent me:<br class=""><br class="">VERSION 5.0.2<br class="">using floats<br class="">version 100, generation 26<br class="">8 atoms<br class="">Traceback (most recent call last):<br class=""> File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",<br class="">line 1747, in __call__<br class=""> File "CHIMERA/share/chimera/baseDialog.py", line 328, in command<br class=""> File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK<br class=""> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply<br class=""> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line<br class="">56, in loadEnsemble<br class=""> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line<br class="">67, in loadEnsemble<br class=""> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25,<br class="">in __init__<br class=""> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86,<br class="">in __init__<br class=""> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line<br class="">345, in _readTopology<br class=""> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line<br class="">338, in _readString<br class=""> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring<br class=""> raise EOFError<br class="">EOFError<br class="">EOFError<br class=""><br class=""> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring<br class=""> raise EOFError<br class=""><br class="">See reply log for Python traceback.<br class=""><br class="">Will be thankful for any suggestions!<br class=""><br class="">Gleb<br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>