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On 8/11/2011 5:36 PM, cuong nguyen wrote:
<blockquote
cite="mid:CAMj9MacaP4fzapyUofNVQwGOpEkSzR1ykT-QZb_mPi+9CAouxA@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
The -ci value for this command would insert more decanol, not mibc.<br>
<br>
<blockquote
cite="mid:CAMj9MacaP4fzapyUofNVQwGOpEkSzR1ykT-QZb_mPi+9CAouxA@mail.gmail.com"
type="cite">
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>
</blockquote>
<br>
Where did mix.gro come from?<br>
<br>
If you want to encourage people to help you, these commands should
be copied and pasted from your terminal (or the shell script you
wrote so that your procedure was self-documenting). Otherwise we've
got no reason to suppose your reported input and your reported
output have any causal relationship between them. The more things
you filter through your head each time, the more errors you will
make - and that goes for more than workflows for getting help! :)<br>
<br>
<blockquote
cite="mid:CAMj9MacaP4fzapyUofNVQwGOpEkSzR1ykT-QZb_mPi+9CAouxA@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
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>
</blockquote>
<br>
The order of the [molecules] section of the grompp -p file must
match the order in the grompp -c file. The order of the atoms within
the [moleculetype] sections must likewise match the order in the
grompp -c file. Yours don't, for some reason. You will have to look
at these orderings and deduce what is wrong.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAMj9MacaP4fzapyUofNVQwGOpEkSzR1ykT-QZb_mPi+9CAouxA@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems"
target="_blank">http://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems</a>
<div><br>
<<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems"
target="_blank">http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems</a>><br>
<br>
<br>
Also possibly useful:<br>
<br>
</div>
<a moz-do-not-send="true"
href="http://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents"
target="_blank">http://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents</a><br>
<<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents</a>><br>
<br>
-Justin<br>
<br>
<br>
-- ==============================__==========
<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>
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href="http://vt.edu" target="_blank">vt.edu</a> <<a
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<br>
-- <br>
Nguyen Van Cuong<br>
PhD student - Curtin University of Technology<br>
Mobile: <a moz-do-not-send="true"
href="tel:%28%2B61%29%20452213981" value="+61452213981"
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</blockquote>
<div>
<div>
<br>
-- <br>
========================================<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" value="+15402319080"
target="_blank">(540) 231-9080</a><br>
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href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
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-- <br>
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<div>PhD student - Curtin University of Technology</div>
<div>Mobile: <a moz-do-not-send="true"
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</blockquote>
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