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Is it a problem with an index file? is 'Water' an index group, and
if so, is is contiguous.<br>
<br>
Erik<br>
<br>
ahmet yıldırım skrev 2011-04-01 14.15:
<blockquote
cite="mid:AANLkTi=ne02q-AEd86O2cW-phhmtAjL5EJP_Y5GeOWM7@mail.gmail.com"
type="cite">I tried SOL 44453 but I still the same error<br>
<br>
<div class="gmail_quote">01 Nisan 2011 15:11 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 text="#000000" bgcolor="#ffffff">
<div class="im"> On 1/04/2011 11:03 PM, ahmet yıldırım
wrote:
<blockquote 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>
</div>
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>
<font color="#888888"> <br>
Mark</font>
<div class="im"><br>
<br>
<blockquote 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"
target="_blank">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>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><br>
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</blockquote>
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<br>
<br clear="all">
<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
</div>
</div>
<br>
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<br>
-- <br>
Ahmet YILDIRIM<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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