<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Are the coordinates identical? Antechamber/Mopac only produces identical charges if the absolute coordinates are identical. Keep in mind that rotating/translating the molecule in Chimera before adding charges will change the absolute coordinates. As for why Antechamber/Mopac is like that, you would have to ask on the Amber mailing list: <a href="http://amber.scripps.edu/%23reflector">The Amber Molecular Dynamics Package</a><div><br></div><div>If you believe the coordinates are identical, make sure that Chimera is determining the element types correctly (Actions->Label->element). If still no difference, send me the files to look at!</div><div><br></div><div>--Eric</div><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><br><div><div>On Aug 29, 2008, at 6:06 AM, Barb Truitt wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>I have two different pdb files that differ only in how the atoms are <br>listed in the atom name columns. In one file all of the Carbon atoms <br>are listed simply as C. In the other file, the carbon atoms are <br>numbered C1, C2, etc. This is true for the other atoms in the <br>molecule, which is not a peptide chain. The mol2 files created by <br>Chimera under the dock prep procedure have different charges assigned <br>to the atoms, differing most in the aromatic carbons. Some of the <br>hydrogens also have different charges assigned to them. Most of the <br>differences are small, but some are 10%. What is the explanation for this?<br><br>Barb Truitt<br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>