<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Eric,<div><br></div><div>That's perfect, worked a treat.</div><div><br></div><div>Thanks for your help.</div><div><br></div><div>Best wishes,</div><div>Kyle<br><div><div>On 30 Jan 2012, at 19:34, 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 Kyle,<div><span class="Apple-tab-span" style="white-space:pre"> </span>The MMTK toolkit that Minimize uses does not have support for bromine currently. Nonetheless there are some parameter files for bromine and iodine obtained from PyMOMO (<a href="http://www.pymomo.de/">http://www.pymomo.de/</a>) that seem reasonable that, if you drop them into the right place in your Chimera distribution, should get your bromonaphthalene minimization to work. For convenience, I've attached the files. The "right place" is <your chimera installation>/lib/python2.7/site-packages/MMTK/Database/Atoms/ [on Windows or Linux] or Chimera.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MMTK/Database/Atoms/ [on Mac].</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Hopefully MMTK will directly support these elements in future releases.</div><div><br></div><div>--Eric</div><div><br><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><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div></div></span></div></div><div><div><div>On Jan 30, 2012, at 12:10 AM, Kyle Morris 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,<div><br></div><div>I get a minimisation error - Atom type "Br" is not supported by MMTK - when trying to minimise a PDB that contains a bromonaphthalene covalently bound ligand. </div><div><br></div><div>I have read the post by <a href="mailto:chimera-users%40cgl.ucsf.edu?Subject=Re:%20%5BChimera-users%5D%20minimization%20error&In-Reply-To=%3CCANgD7bEi-xXuz%3Dc--MtP-O1-o1ifO8MDeaz89OkTb-JHsSBYbg%40mail.gmail.com%3E" title="[Chimera-users] minimization error" style="font-family: Times; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); font-size: medium; ">neelagiri.d at gmail.com </a> and note the Cl substitution does make this work but my Br is part of the molecule and so GAFF/Antechamber should be able to handle it I thought?</div></div></blockquote><br></div></div><div></div><span><br></span></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><span><i></span></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><div apple-content-edited="true"><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-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; "><br class="Apple-interchange-newline"></div></span> </div><br></div>_______________________________________________<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></blockquote></div><br></div></body></html>