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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>What is the contents of the HO.itp 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>&nbsp;</o:p></span></p>

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<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 9909 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>

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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><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>#ZHAO LINA#<br>
<b>Sent:</b> Tuesday, 14 September 2010 2:53 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> RE: [gmx-users] how to let the grompp finding library
fromworkingdirectory first.<o:p></o:p></span></p>

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<p class=MsoNormal><o:p>&nbsp;</o:p></p>

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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:black'>Yes.&nbsp; <br>
<br>
I did it already. But it did not work.<br>
in topol.top file,<br>
;Include topology<br>
#include &quot;HO.itp&quot;<br>
<br>
Thanks,<br>
<br>
lina<o:p></o:p></span></p>

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<p class=MsoNormal style='margin-bottom:12.0pt'><b><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif";color:black'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>
gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of
Dallas Warren [Dallas.Warren@monash.edu]<br>
<b>Sent:</b> Tuesday, September 14, 2010 12:48 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> RE: [gmx-users] how to let the grompp finding library from
workingdirectory first.</span><span style='color:black'><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'>What is the contents of your topol.top and HO.itp file?&nbsp;
Does the topol.top &#8220;include&#8221; the HO.itp in it?</span><span style='color:black'><o:p></o:p></span></p>

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

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>To have an &#8220;included topology file&#8221; (.itp) file processed by
grompp, it has to be directed to it.&nbsp; This is typically done by using a
#include &#8220;HO.itp&#8221; line within the topol.top file.</span><span style='color:
black'><o:p></o:p></span></p>

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

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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren</span><span style='color:black'><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</span><span
style='color:black'><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, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu</span><span style='color:black'><o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>+61 3 9909 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'> </span><span style='color:black'><o:p></o:p></span></p>

</div>

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

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border-color:-moz-use-text-color -moz-use-text-color -moz-use-text-color blue'>

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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:black'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:black'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>#ZHAO LINA#<br>
<b>Sent:</b> Tuesday, 14 September 2010 2:33 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] how to let the grompp finding library from
workingdirectory first.</span><span style='color:black'><o:p></o:p></span></p>

</div>

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<p class=MsoNormal><span style='color:black'>&nbsp;<o:p></o:p></span></p>

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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:black'>Hi,<br>
<br>
The HO atom type was in the working directory .itp file.<br>
How can I let the grompp work from searching the library of the working
directory, not like this:<br>
<br>
grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr<br>
<br>
<br>
checking input for internal consistency...<br>
processing topology...<br>
Opening library file /usr/share/gromacs/top/ff_dum.itp<br>
Generated 165 of the 1596 non-bonded parameter combinations<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.7<br>
Source code file: ../../../../src/kernel/toppush.c, line: 947<br>
<br>
Fatal error:<br>
Atomtype HO not found<br>
-------------------------------------------------------<br>
<br>
Do I need add something in minim.mdp? Or maybe just some parts wrong I do not
realise.<br>
<br>
Thanks and best regards,<br>
<br>
lina</span><span style='color:black'><o:p></o:p></span></p>

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