<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Eric,<div><br></div><div>Many thanks for the immediate reply. Chimera 1.6 works perfectly well. </div><div><br></div><div>Best regards</div><div><br></div><div>George</div><div><br></div><div><br><div><div>On Nov 28, 2011, at 8:17 PM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi George,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Support for the prmtop format used by AmberTools 1.5 was added since the Chimera 1.5.3 release, therefore you need to download the 1.6 daily build to read your trajectory.</div><div><br></div><div>--Eric</div><div><br></div><div>P.S. Thanks for making your trajectory available. That made it very easy to determine the problem.</div><div><br></div><div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu/">http://www.cgl.ucsf.edu</a></font></div><div><br></div></div></span></div></div><div><br><div><div>On Nov 28, 2011, at 11:01 AM, George Tzotzos wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Elaine,<br><br>Many thanks for this. Unfortunately the files are too big to email them. I'd be grateful if you and/or your colleagues could download them from the following link.<br><br><a href="http://dl.dropbox.com/u/50952643/2erb-IND-traj.zip">http://dl.dropbox.com/u/50952643/2erb-IND-traj.zip</a><br><br>I'm using Chimera version 1.5.3 (build 33475). My operating system is OSX 1.6.8 on a 2x2.93 GHz 6-Core Intel Xeon machine.<br><br>Many thanks in advance for all the help.<br><br>George<br><br>On Nov 28, 2011, at 6:24 PM, Elaine Meng wrote:<br><br><blockquote type="cite">Hi George,<br></blockquote><blockquote type="cite">The better approach to report Chimera problems is with Help... Report a bug in the menu, or this web form.<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py">http://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py</a>><br></blockquote><blockquote type="cite"> It will let you attach a file (and include your email address if you want feedback). <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In this case the trajectory file would be more useful than the error message. Also, I guess we would need both prmtop and trajectory, and I'm not sure if the approach above would let you attach both, so yet another possibility is to send email to <a href="mailto:chimera-bugs@cgl.ucsf.edu">chimera-bugs@cgl.ucsf.edu</a> and attach both those files. Please also mention your Chimera version and what kind of computer you are using (e.g. Windows, Mac ...).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite">----------<br></blockquote><blockquote type="cite">Elaine C. Meng, Ph.D. <br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></blockquote><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote><blockquote type="cite">University of California, San Francisco<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Nov 28, 2011, at 2:37 AM, George Tzotzos wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">The error was "TypeError: Attempt to form duplicate covalent bond."<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Best regards<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">George<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div><br><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 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></div><br class="Apple-interchange-newline"></div></span> </div><br></div></blockquote></div><br></div></body></html>