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><br><br><br><div class="gmail_quote">01 Nisan 2011 14:41 tarihinde Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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><div></div><div class="h5">On 1/04/2011 10:26 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 Justin,<br>
<br>
I have Fatal Errror:The solvent group Water is not continuous. I look at gmx-users mailing list search. I also have the same problem.<br>
You 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 solvent, ligand, then<br>
solvent. To use genion (as the program prints out at the prompt) you must have<br>
a *continuous* group of solvent in order to embed ions. If you re-arrange the<br>
<br>
coordinate file and [molecules] section of the topology, you can achieve this.<br>
<br>
How can I do the re-arrange you said? Can you explain a little bit?<br>
</blockquote>
<br></div></div>
You need a system topology whose molecules are ordered such that all the water is contiguous. That means the order of the names of molecule types in your [ molecules ] section of your .top can have only one mention of water. Since the order of molecules in the coordinate file must match this order, you will need to physically reorder your [ molecules ] section, and the chunks of molecules in your coordinate file. Fortunately, you don't have to renumber those atoms in the coordinate file.<br>
<font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>