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<div style="">Yes. <br>
<br>
I did it already. But it did not work.<br>
in topol.top file,<br>
;Include topology<br>
#include "HO.itp"<br>
<br>
Thanks,<br>
<br>
lina<br>
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<div style="direction: ltr;" id="divRpF525924"><font size="2" color="#000000" face="Tahoma"><b>From:</b> 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.<br>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">What is the contents of your topol.top and HO.itp file? Does the topol.top “include” the HO.itp in it?</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">To have an “included topology file” (.itp) file processed by grompp, it has to be directed to it. This is typically done by using a #include “HO.itp”
line within the topol.top file.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
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<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Medicinal Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Monash Institute of Pharmaceutical Sciences</span><span style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">+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: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">
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<p class="MsoNormal"><b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span style="font-size: 10pt; 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 2:33 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></p>
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<p class="MsoNormal"><span style="font-size: 10pt; 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></p>
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