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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'>Please copy and paste in here the contents of your .top file.<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>mustafa bilsel<br><b>Sent:</b> Friday, 7 January 2011 12:32 PM<br><b>To:</b> gmx-users@gromacs.org<br><b>Subject:</b> [gmx-users] methanol simulation error<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi all, <br>I try to make a simulation in methanol. I use gromos43a1 forcefield.<br>My command follow,<br>pdb2gmx -f xxx.pdb<br>editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro<br>genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro<br>When grompp for minimization it gives an error:<br>Atomtype CMET not found<br><br>I have used grep to count the methanol molecules and added SOL 660 comment in .top file to tell the number of methanols. <br>Also I added #include "gromos43a1.ff/methanol.itp" line to .top.<br><br>Please don't suggest non-water solvation in how-to part of Gromacs web.<br><br>Could you tell me what missing is?<br><br>best wishes<br>mustafa <o:p></o:p></p></div></div></body></html>