<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Christos,<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>The Gasteiger implementation in Antechamber (which Chimera uses for partial-charge calculation) ignores the formal charge specification -- which is a bug that I believed I've reported to the Antechamber developers at least once but I guess I'll report it again.</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>If you must use Gasteiger charges, at least some of the alternatives include the PETRA server run by the Gasteiger group itself:</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN></DIV><DIV><A href="http://www2.chemie.uni-erlangen.de/services/petra/index.html">http://www2.chemie.uni-erlangen.de/services/petra/index.html</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>and OpenBabel:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><A href="http://openbabel.sourceforge.net/wiki/Capabilities">http://openbabel.sourceforge.net/wiki/Capabilities</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV> <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>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>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="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></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><BR><DIV><DIV>On Aug 2, 2007, at 12:29 PM, <A href="mailto:cdeligka@purdue.edu">cdeligka@purdue.edu</A> wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dear all,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I tried to calculate the Gasteiger charges of peroxynitrite anion using Chimera</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(I tried the version that was recently released as well as some previous ones).</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">This is my PDB file:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">HEADER</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">HETATM<SPAN class="Apple-converted-space"> </SPAN>1<SPAN class="Apple-converted-space"> </SPAN>O <SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>1.225 <SPAN class="Apple-converted-space"> </SPAN>0.000 <SPAN class="Apple-converted-space"> </SPAN>1.819</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">HETATM<SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>N <SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>0.138 <SPAN class="Apple-converted-space"> </SPAN>0.000 <SPAN class="Apple-converted-space"> </SPAN>1.281</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">HETATM<SPAN class="Apple-converted-space"> </SPAN>3<SPAN class="Apple-converted-space"> </SPAN>O <SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>0.138 <SPAN class="Apple-converted-space"> </SPAN>0.000<SPAN class="Apple-converted-space"> </SPAN>-0.086</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">HETATM<SPAN class="Apple-converted-space"> </SPAN>4<SPAN class="Apple-converted-space"> </SPAN>O <SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>2<SPAN class="Apple-converted-space"> </SPAN>1.359 <SPAN class="Apple-converted-space"> </SPAN>0.000<SPAN class="Apple-converted-space"> </SPAN>-0.746</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The formal charge of this molecule is -1.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">For some reason Chimera generates the Gasteiger charges for the molecule but</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">these charges correspond to a formal charge of zero and not -1.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">If I try the other method AM1-BCC the charges that are calculated do correspond</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">to a formal charge of -1.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">In my calculations I do need the Gasteiger charges and so I cannot use the ones</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">that are calculated by AM1-BCC.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">If you have any suggestions please let me know.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Are you aware of any other software that might be able to do this calculation?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thank you all,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Christos</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>