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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>If you have the pKa for each of those three groups, then you can calculate that yourself very quickly.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Catch ya,<br><br>Dr. Dallas Warren<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Medicinal Chemistry and Drug Action<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>, Monash University<br>381 Royal Parade, Parkville VIC 3010<br>dallas.warren@monash.edu<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>+61 3 9903 9304<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>Nancy<br><b>Sent:</b> Monday, 10 January 2011 10:12 AM<br><b>To:</b> Discussion list for GROMACS users<br><b>Subject:</b> [gmx-users] Pioglitazone Tautomers<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:12.0pt'>Hi All,<br><br>I am performing molecular docking and molecular dynamics simulations of the thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous different tautomeric states; I have attached a figure depicting several of them. Which tautomer would be dominant at the physiological pH of ~7.0?<br><br>Also, are there any software programs that can predict which tautomer would be correct?<br><br>Thanks in advance,<br>Nancy<br><br><o:p></o:p></p></div></div></body></html>