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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">&lt;<a moz-do-not-send="true"
            href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;</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">&lt;<a
                      moz-do-not-send="true"
                      href="mailto:Mark.Abraham@anu.edu.au"
                      target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</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>
                        -- <br>
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                    </div>
                  </blockquote>
                </div>
                <br>
                <br clear="all">
                <br>
                -- <br>
                Ahmet YILDIRIM<br>
              </blockquote>
              <br>
            </div>
          </div>
          <br>
          --<br>
          gmx-users mailing list    <a moz-do-not-send="true"
            href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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        </blockquote>
      </div>
      <br>
      <br clear="all">
      <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>
</pre>
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