When I created em.tpr I got the followings notes:<br><b><u>NOTE 1 [file topol.top, line 52]:</u></b><br> System has non-zero total charge: -1.500000e+01<br>
<br><u><b>NOTE 2 [file topol.top]:</b></u><br> The largest charge group contains 11 atoms.<br> Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br>
groups can lead to serious cut-off artifacts.<br> For efficiency and accuracy, charge group should consist of a few atoms.<br> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>then, I tried to add ions.<br>
<br>Thanks<br><br><div class="gmail_quote">01 Nisan 2011 15:33 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> yazdı:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear users,<br>
<br>
I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.<br>
<br>
</blockquote>
<br></div>
...and hopefully did a complete re-parameterization of the nonsense charges it gives.<br>
<br>
<a href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips" target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a><br>
<br>
That's an aside, completely unrelated to your actual problem, though.<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log<br>
select group:13<br>
Fatal error:<br>
The solvent group SOL is not continuous: index[984]=5334, index[985]=5355<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
</blockquote>
<br></div>
You still haven't answered the second question I posed below. I assume this "em.tpr" file has not been re-generated from a properly continuous .gro and .top combination. If either were out of order with respect to the other (i.e. changing the .top and not the .gro), you would have gotten a fatal error from grompp when creating em.tpr.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
01 Nisan 2011 15:17 tarihinde 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>>> yazdı:<div><div>
</div><div><br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
I tried SOL 44453 but I still the same error<br>
<br>
<br>
Are you using some index file that is specifying a discontinuous<br>
water group? Have you properly re-created your genion input .tpr<br>
file from this new topology?<br>
<br>
-Justin<br>
<br>
01 Nisan 2011 15:11 tarihinde Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>> yazdı:<br>
<br>
<br>
On 1/04/2011 11:03 PM, ahmet yıldırım wrote:<br>
<br>
Dear Dr. Mark,<br>
<br>
I did you said but I have the same error. please look at<br>
attached file<br>
<br>
topol.top:<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1<br>
Protein_chain_B 1<br>
SOL 185<br>
SOL 143<br>
SOL 44125<br>
TRS 1<br>
EDO 1<br>
<br>
<br>
OK, well maybe it doesn't like different chunks of the same<br>
molecule<br>
even when they're adjacent in order. Try "SOL 44453" instead.<br>
<br>
Mark<br>
<br>
<br>
01 Nisan 2011 14:41 tarihinde Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>> yazdı:<br>
<br>
<br>
On 1/04/2011 10:26 PM, ahmet yıldırım wrote:<br>
<br>
Dear Justin,<br>
<br>
I have Fatal Errror:The solvent group Water is not<br>
continuous. I look at gmx-users mailing list<br>
search. I<br>
also have the same problem.<br>
You<br>
said:(<a href="http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html</a>)<br>
It is exactly what I said; you've proven it. You have<br>
solvent, ligand, then<br>
solvent. To use genion (as the program prints out<br>
at the<br>
prompt) you must have<br>
a *continuous* group of solvent in order to embed<br>
ions. If<br>
you re-arrange the<br>
<br>
coordinate file and [molecules] section of the<br>
topology,<br>
you can achieve this.<br>
<br>
How can I do the re-arrange you said? Can you<br>
explain a<br>
little bit?<br>
<br>
<br>
You need a system topology whose molecules are<br>
ordered such<br>
that all the water is contiguous. That means the<br>
order of the<br>
names of molecule types in your [ molecules ] section<br>
of your<br>
.top can have only one mention of water. Since the<br>
order of<br>
molecules in the coordinate file must match this<br>
order, you<br>
will need to physically reorder your [ molecules ]<br>
section,<br>
and the chunks of molecules in your coordinate file.<br>
Fortunately, you don't have to renumber those atoms<br>
in the<br>
coordinate file.<br>
<br>
Mark<br>
<br>
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<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><div></div><div><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote><div><div></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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>