<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jul 28, 2010, at 8:03 AM, Jon Rumbley wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>I have several small organic molecules constructed in ChemDraw and converted<br>in Chem3D to .mol2 files. I can open them in Chimera but cannot seem to add<br>charges to. I was simply using the add charge menu commands and AM1-BCC and<br>assuming the structures would be read as nonstandard but antechamber reports<br>an error with residue ****. The error log has no real indication of what the<br>trouble might be. Are there additional steps I must take before assigning<br>charges? The structures already have hydrogens added. An example .mol2 file<br>is below:<br></div></blockquote></div><br><div>Hi Jon,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Using the file you provided (and that I've attached) I get no error in Chimera 1.4.1 nor the 1.5 daily build (though the latter is <i>much</i> slower due to the newer version of AmberTools using sqm to compute charges rather than mopac). Can you tell me what version of Chimera you're using and what platform you're running it on? Thanks!</div><div><br></div><div>--Eric</div><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></body></html>