Dear users,<br><br>I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.<br><br>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">http://www.gromacs.org/Documentation/Errors</a><br><br><br><br><div class="gmail_quote">
01 Nisan 2011 15:17 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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 class="im"><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;">
I tried SOL 44453 but I still the same error<br>
<br>
</blockquote>
<br></div>
Are you using some index file that is specifying a discontinuous water group? Have you properly re-created your genion input .tpr file from this new topology?<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;">
01 Nisan 2011 15:11 tarihinde Mark Abraham <<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>>> yazdı:<div class="im">
<br>
<br>
On 1/04/2011 11:03 PM, 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 Dr. Mark,<br>
<br>
I did you said but I have the same error. please look at 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>
</blockquote>
<br>
OK, well maybe it doesn't like different chunks of the same molecule<br>
even when they're adjacent in order. Try "SOL 44453" instead.<br>
<br>
Mark<br>
<br>
<br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
01 Nisan 2011 14:41 tarihinde Mark Abraham<br></div>
<<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>>> yazdı:<div><div></div><div class="h5">
<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 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 at the<br>
prompt) you must have<br>
a *continuous* group of solvent in order to embed ions. If<br>
you re-arrange the<br>
<br>
coordinate file and [molecules] section of the topology,<br>
you can achieve this.<br>
<br>
How can I do the re-arrange you said? Can you explain a<br>
little bit?<br>
<br>
<br>
You need a system topology whose molecules are ordered such<br>
that all the water is contiguous. That means the order of the<br>
names of molecule types in your [ molecules ] section of your<br>
.top can have only one mention of water. Since the order of<br>
molecules in the coordinate file must match this order, you<br>
will need to physically reorder your [ molecules ] section,<br>
and the chunks of molecules in your coordinate file.<br>
Fortunately, you don't have to renumber those atoms in the<br>
coordinate file.<br>
<br>
Mark<br>
<br>
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</div></blockquote><div class="im">
<br>
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</div></blockquote>
<br>
-- <br><div class="im">
========================================<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>
<br>
========================================<br>
-- <br></div><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>