Dear,<br><br>I created a 5 5 2 box containing 15 mibc and 15 decanol molecues by using two comands:<br><i>genbox -ci decanol.gro -nmol 15 -box 5 5 2 -o layer.gro -p decanol.top<br>genbox -cp layer.gro -ci decanol.gro -nmol 15 -box 5 5 2 -o box.gro -p mibc.top</i><br>
then I filled this mixture by water to create other 5 5 10 box by using comands:<br><i>genbox -cp mix.gro -cs spc216.gro -o box1.g96 -p topol.top -box 5 5 10</i><br><br>the topol.top file is: <br><br><i>#include "ffG43a1.itp"<br>
#include "decanol.itp"<br><br>#include "mibc.itp"<br><br>; include water<br>#include "spce.itp"<br><br>[ system ]<br>MIBC and dec in water<br><br>[ molecules ]<br>dec 15<br>mibc 15<br><br>sol 7947.</i><br>
<br>then I ran the grompp comand: grompp -f input_min.mdp -o min.tpr -c box1.g96 and the errors was<br><br>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 2 in topol.top and
box1.g96 does not match (CAC - CAF)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 3 in topol.top and
box1.g96 does not match (CAE - CAB)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 4 in topol.top and
box1.g96 does not match (CAG - CAE)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 5 in topol.top and
box1.g96 does not match (CAI - CAG)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 6 in topol.top and
box1.g96 does not match (CAK - CAC)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 7 in topol.top and
box1.g96 does not match (CAJ - OAD)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 8 in topol.top and
box1.g96 does not match (CAH - HAN)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 9 in topol.top and
box1.g96 does not match (CAF - CAA)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Warning: atom name 10 in topol.top and
box1.g96 does not match (CAD - CAF)</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">WARNING 1 [file topol.top, line 20]:</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US"><span>
</span>220 non-matching atom names</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US"><span>
</span>atom names from topol.top will be used</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US"><span>
</span>atom names from box1.g96 will be ignored</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">---------------------------------------------------<br></span></i></p><p class="MsoNormal"><i><span lang="EN-US">Fatal error:</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">Too many warnings (2), grompp terminated.</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">If you are sure all warnings are harmless,
use the -maxwarn option.</span></i></p>
<p class="MsoNormal"><i><span lang="EN-US">For more information and tips for
troubleshooting, please check the GROMACS</span></i></p>
<i><span style="font-size:12.0pt;font-family:Cambria" lang="EN-US">website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></span>
</i><br><br>Please help me to correct these errors.<br><br>Thank you very much<br><br>best regards,<br><br>Cuong<br><br><div class="gmail_quote">2011/11/7 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br>
<br>
cuong nguyen wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear,<br>
<br>
Thanks a lot Justin. I created a box containing mixed solution of 20 hexanol molecues and 20 octanol molecules in water. However, when I run grompp and mdrun commands, gromacs noticed errors with the topol.top file for this mixed system.<br>
<br>
So please help me to create a suitable topol.top file to this system.<br>
<br>
</blockquote>
<br></div>
No one can help you without knowing the exact errors that grompp produced.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
Thanks a lot.<br>
<br>
Best regards,<br>
<br>
<br>
Cuong<br>
<br></div>
2011/11/7 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><br>
<br>
<br>
<br>
Justin A. Lemkul wrote:<br>
<br>
<br>
<br>
cuong nguyen wrote:<br>
<br>
Dear,<br>
<br>
I would like to create a solution of mix substances (hexanol<br>
and octanol) in water. I got top files and gro files of<br>
these alcohols from PRODRG server. However I do not know how<br>
to mix these top file to create topol.top file for this mixture.<br>
<br>
<br>
Please read the tutorial:<br>
<br></div>
<a href="http://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems" target="_blank">http://www.gromacs.org/__<u></u>Documentation/Tutorials#__<u></u>Heterogeneous_Systems</a><div><br>
<<a href="http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems" target="_blank">http://www.gromacs.org/<u></u>Documentation/Tutorials#<u></u>Heterogeneous_Systems</a>><br>
<br>
<br>
Also possibly useful:<br>
<br></div>
<a href="http://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents" target="_blank">http://www.gromacs.org/__<u></u>Documentation/How-tos/Mixed___<u></u>Solvents</a><br>
<<a href="http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/Mixed_<u></u>Solvents</a>><br>
<br>
-Justin<br>
<br>
<br>
-- ==============================<u></u>__==========<div><br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<tel:%28540%29%20231-9080><br>
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-- <br>
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Mobile: <a href="tel:%28%2B61%29%20452213981" value="+61452213981" target="_blank">(+61) 452213981</a><br>
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<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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