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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>It seems the ions type not set.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<div>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Best regards</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Yuguang</span></font><font color=navy><span
style='color:navy'><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=3 color=navy face=SimSun><span style='font-size:
12.0pt;color:navy'>&nbsp;<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dr. Yuguang Mu</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Assistant Professor</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>

<p class=MsoNormal><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=2
  color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
  color:navy'>School</span></font></st1:PlaceType><font size=2 color=navy
 face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'> of <st1:PlaceName
 w:st="on">Biological</st1:PlaceName></span></font></st1:place><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> Sciences</span></font><font color=navy><span style='color:navy'><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Nanyang Technological University</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>

<p class=MsoNormal><st1:Street w:st="on"><st1:address w:st="on"><font size=2
  color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
  color:navy'>60 Nanyang Drive</span></font></st1:address></st1:Street><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>&nbsp; <st1:country-region w:st="on"><st1:place w:st="on">Singapore</st1:place></st1:country-region>
637551 Tel: +65-63162885 Fax: +65-67913856</span></font><font color=navy><span
style='color:navy'><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><a
href="http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php">http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php</a></span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=3 color=navy face=SimSun><span style='font-size:
12.0pt;color:navy'>&nbsp;</span></font><o:p></o:p></p>

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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>job560@sohu.com<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, April 06, 2007 10:15
AM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] Can you help
me ?</span></font><o:p></o:p></p>

</div>

<p class=MsoNormal><font size=3 face=SimSun><span style='font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p><font size=3 face=SimSun><span style='font-size:12.0pt'>when I use the
following command&nbsp;,there always a error message.Can you help me ? Thank
you very much !<o:p></o:p></span></font></p>

<p><font size=3 face=SimSun><span style='font-size:12.0pt'>command: <font
color=red><span style='color:red'>grompp -f em.mdp -c trp_b4em.gro -p trp.top
-o trp_em.tpr</span></font><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<o:p></o:p></span></font></p>

<p><font size=3 face=SimSun><span style='font-size:12.0pt'>error message:<br>
&nbsp;&nbsp; .<br>
&nbsp;&nbsp; .<br>
creating statusfile for 1 node...<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br>
checking input for internal consistency...<br>
calling /usr/bin/cpp...<br>
processing topology...<br>
Generated 279 of the 1225 non-bonded parameter combinations<br>
Excluding 3 bonded neighbours for Protein 1<br>
Excluding 3 bonded neighbours for IN4 1<br>
Excluding 2 bonded neighbours for SOL 4145<br>
Cleaning up temporary file gromppD2IkOr<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3<br>
Source code file: toppush.c, line: 1264<br>
Fatal error:<br>
No such moleculetype Cl<br>
-------------------------------------------------------<o:p></o:p></span></font></p>

<p><font size=3 face=SimSun><span style='font-size:12.0pt'>&nbsp;<o:p></o:p></span></font></p>

<p><font size=3 face=SimSun><span style='font-size:12.0pt'>enviroment:<o:p></o:p></span></font></p>

<p><font size=3 face=SimSun><span style='font-size:12.0pt'><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>
extra information:<br>
&nbsp;&nbsp;&nbsp;&nbsp; OS:&nbsp; Red Hat Linux AS4<br>
&nbsp;&nbsp; fftw:&nbsp; fftw-3.1.2.tar.tar<br>
gromacs:&nbsp; gromacs-3.3.tar.gz<o:p></o:p></span></font></p>

<p><font size=3 face=SimSun><span style='font-size:12.0pt'>installation :<br>
1.fftw<br>
./configure --enable-float<br>
make<br>
make install <br>
2. gromacs<br>
./configure&nbsp;&nbsp;&nbsp;
CPPFLAGS=&quot;-I/gromacs/gromacs-3.3/include&quot;&nbsp; LDFLAGS=&quot;-L/gromacs/fftw-3.1.2/libbench2&quot;&nbsp;
<br>
make <br>
make install<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3 face=SimSun><span
style='font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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face=SimSun><span style='font-size:12.0pt'>

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