<html><body 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; 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; -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"><http://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py><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 chimera-bugs@cgl.ucsf.edu 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>Chimera-users@cgl.ucsf.edu<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; 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></body></html>