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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>For anyone to have a chance to help you, you are going to have
to provide more details than simply stating &#8220;blew up&#8221;.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>What command line did you use, actually paste it in here?&nbsp; What
molecule / protein?&nbsp; What forcefield?&nbsp; Paste the actual output from the command
in here, showing exactly what you mean by &#8220;blew up&#8221;.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

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<p class=MsoNormal align=left style='text-align:left'><span style='font-size:
10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Medicinal Chemistry and Drug Action<br>
</span><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<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>

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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

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<p class=MsoNormal align=left style='text-align:left'><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>Hao Sun<br>
<b>Sent:</b> Monday, 26 July 2010 12:36 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] hydrogen-bonded complex<o:p></o:p></span></p>

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<p class=MsoNormal align=left style='text-align:left'><o:p>&nbsp;</o:p></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'>Dear
all,<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'>I
am trying to simulate a hydrogen-bonded complex. When I treated the pdb file
with pdb2gmx, the structure of gro file blew up. Could you give me some hint on
what the potential problem is? What and in which file should I give some
specification for hydrogen bonding? Many thanks.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'>With
best regards.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'>Yours
sincerely,<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'>Hao
Sun<o:p></o:p></span></p>

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