<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Right. I was computing the π electrons contributed to the ring by the nitrogens incorrectly. The fix will be in tonight's daily build. BTW, your file does have 26 lines -- the last line contains a single space character.<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 Sep 15, 2008, at 7:39 AM, Francesco Pietra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi:<br>I am dealing with pyrazine compunds in view of docking with DOCK6. The<br>two nitrogens proved problematic for Chimera so that, to simplify, I<br>tried with pyrazine itself, getting the same problems.<br><br>I used for getting the pdb the MM package I am familiar with:<br>1. draw benzene,<br>2. replace two para carbons with N,<br>3. replace the H on N with a lone pair.<br><br>The two nitrogens are now indicated of MM3 (or MMX) type 37 (-N=C-/PYR<br>(DELOCALIZED). The charge on the nitrogens is 0.15, on the lone pairs<br>-0.21, on carbon 0.14, on H 0.04.<br><br>Save as pdb, load to Chimera, then Tools, Structure editing .. Add<br>charge, it results total charge -2. In fact, commanding addH adds a<br>hydrogen to each nitrogen and the resulting molecule is neutral, while<br>it should be +2.<br><br>If in Chimera I save the loaded pdb as mol2, the two nitrogens result<br>of Tripos type N.pl3, i.e., trigonal planar nitrogen, which is the<br>wrong type. Naively, I replaced N.pl3 with N.ar (aromatic nitrogen) in<br>the mol2.file, getting the same results on reloading the mol2.<br><br>So the two packages, MM and Chimera are internally consistent but (for<br>the first time in my experience with both packages) they are not<br>mutually consistent.<br><br>I tried to build pyrazine atom-by-atom, getting the same results.<br><br>Attached is the pdb and the mol2. When opening the pdb, Chimera says:<br>"Ignored bad pdb record found on line 26"; actually there are fewer<br>than 26 lines.<br><br>Thanks for help<br><br>francesco pietra<br><span><pyrazine.pdb></span><span><pyrazine.mol2></span>_______________________________________________<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>