<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Francesco,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Unfortunately Chimera doesn't support the prmtop/DCD combo. The only possibility I can find is to convert your prmtop to a psf in VMD as described in this mail (option "a"):</div><div><br></div><div><a href="http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14106.html">http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14106.html</a></div><div><br></div><div>But at that point you are already using VMD and I don't see why you wouldn't just go ahead and visualize your trajectory using that instead of relying on the shaky prmtop->psf conversion.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I will open a feature-request ticket in our Trac database for allowing "mix and match" of topology/coordinate formats, with you on the recipient list.</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 Mar 2, 2010, at 3:43 AM, Francesco Musiani wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi all,<br>I would like to visualize in Chimera a trajectory obtained with the program NAMD,<br>but I have a .prmtop topology file generated using AMBER instead of a .psf topology file.<br><br>I have these files beacuse in NAMD is possible to use AMBER format topology.<br><br>Is it possible to implement an additional feature in Chimera which allows to visualize<br>NAMD trajectory using AMBER topology?<br><br>Thanks in advance,<br><br>Francesco</div></blockquote></div></div></body></html>