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On 1/04/2011 11:03 PM, ahmet yıldırım wrote:
<blockquote
cite="mid:AANLkTimK2svOJfSNhfecY4MxBJsrVjttOdYt+e8JnkXC@mail.gmail.com"
type="cite">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
even when they're adjacent in order. Try "SOL 44453" instead.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTimK2svOJfSNhfecY4MxBJsrVjttOdYt+e8JnkXC@mail.gmail.com"
type="cite">
<div class="gmail_quote">01 Nisan 2011 14:41 tarihinde Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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 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 moz-do-not-send="true"
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 class="h5"><br>
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</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
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