<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Christos,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Unfortunately this is an underlying problem of the antechamber program (from AmberTools) that Chimera is using. When computing Gasteiger charges antechamber ignores the charge specified (with the -nc flag) and instead bases the charge on what its estimate of the Gasteiger atoms types of the molecule are. I have complained about this on the Amber mailing list (e.g. <a href="http://archive.ambermd.org/201006/0627.html)">http://archive.ambermd.org/201006/0627.html)</a> but so far the behavior remains unchanged. I suggest you complain on the list as well -- the squeaky wheel gets the grease.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I'm sorry I don't have anything more useful to offer (except to suggest using AM1-BCC charges instead).</div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><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-size: 16px; "><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-size: 16px; "><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><div>On Mar 15, 2012, at 8:17 AM, Christos Deligkaris wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Chimera users,<br><br>I have a charged ligand (formal charge of +2) and I have tried using Chimera to calculate the partial charges of that molecule.<br><br>Even though Chimera predicts correctly that the net charge is +2, after calculating the partial charges (using the Gasteiger method) I see that the sum of all partial charges is zero.<br> <br>Changing the net charge of the molecule seems to have no effect on the calculation of the partial charges.<br><br>It also seems that the Gasteiger website does not offer the service of calculating the partial charges any more... (<a href="http://www2.chemie.uni-erlangen.de/services/petra/smiles.html">http://www2.chemie.uni-erlangen.de/services/petra/smiles.html</a>)<br> <br>Do you have any suggestions on how to calculate the Gasteiger charges so that the net charge on my molecule is +2?<br><br>Thank you for your help,<br clear="all"><br>-- <br>Christos<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></blockquote></div><br></div><br><br><div apple-content-edited="true"> </div><br></body></html>