<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Oct 13, 2011, at 1:29 PM, Ibrahim Moustafa wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <title>Gasteiger charge</title> <div> <font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">Dear Chimera developers:<br> <br> I want to assign Gasteiger charges for a ligand, as a preparative step for docking. The ligand is GTP, extracted from a protein complex structure.<br> <br> I wanted to add the Gasteiger partial charge, and explicitly chose to have a total charge of “-4” on the ligand molecule. However, the program assigned partial charges that sum to total charge of “-2” instead of “-4”.<br> <br> Any idea why the program assigned the Gasteiger partial charges incorrectly, ignoring the input total charge on the ligand.</span></font></div></blockquote><br></div><div>Amber's antechamber program (which Chimera uses for charge assignment) does not honor the '-nc' flag (net charge) for Gasteiger charges. It just uses what it believes the charge to be, which I guess in this case is -2 (weird choice!). You can see complaints about this if you google for "gasteiger" along with "nc".</div><div><br></div><div>If you use the latest daily build (tomorrow's!) then you can use AM1-BCC charges for GTP. We've added "charge templates" for GTP/GDP/ADP/ATP since antechamber frequently fails with highly negatively-charged systems, so we used charges taken from the <a href="http://www.pharmacy.manchester.ac.uk/bryce/amber/">Amber parameter database</a> for those commonplace residues. However, in constructing the template for GTP I missed HO3', so that's why you would need to get tomorrow's build.</div><br><div>Finally, you should probably use AddH separately and see if Chimera adds a proton to the terminal phosphate of your GTP. If it does, delete it before adding charges. The template charges are for GTPs with no protonation on the terminal phosphate.</div><div><br></div><div>--Eric</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>