<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Dear Chimera-users,<br > <br > Hello, I am a brand new entry into this forum. I have started using chimera recently. I use Gromacs for my molecular modeling work. Till I become friendly with chimera I need your valuable suggestions and cooperations. I request you to kindly bear with my very silly doubts and questions. Let me explain my problem.<br > I have a protein of 35 residues and have simulated in a box of water for 10ns. My protein has charge so in order to neutralize it I have added counterions randomly placed them in the solvent(water). The counter ions that I am adding are Cl- ions. I have created a *.trr file of the tracjectory for this 10ns. I would like to visulaize this trajectory using chimera. I am using Tools /MD/Ensemble Analysis /MD Movie to load the trr file. when I do so I am getting the following error:<br ><br ><font size="4"><SPAN STYLE="font-style: italic;">Unknown molecule type: CL-</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">TypeError: __len__() should return an int</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">(see reply log for Python traceback info)</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">Traceback (most recent call last):</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "/usr/local/chimera/share/__main__.py", line 59, in ?</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> value = chimeraInit.init(sys.argv)</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/chimeraInit.py", line 318, in init</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> tkgui.eventLoop()</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/chimera/tkgui.py", line 2675, in eventLoop</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/lib/python2.4/lib-tk/Tkinter.py", line 965, in mainloop</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> self.tk.mainloop(n)</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/chimera/baseDialog.py", line 231, in <lambda></SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/chimera/baseDialog.py", line 473, in OK</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 87, in Apply</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 30, in __init__</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 218, in __init__</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 229, in _readHeader</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> File "CHIMERA/lib/python2.4/xdrlib.py", line 194, in unpack_fstring</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;"> if j > len(self.__buf):</SPAN><br style="font-style: italic;" ><SPAN STYLE="font-style: italic;">TypeError: __len__() should return an int</SPAN></font><br ><br >What exactly is the problem ? How to solve it ?<br ></BODY></HTML>