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    Having only browesd through the papaer very briefly, I can't see how
    the protonation state was chosen. The modelling part of the paper
    wasn't that informative. There is a web service called H++ that can
    make pKa estimates for titrating sites. Not sure how accurate it is
    though. It uses continuum electrostatics that may not be accurate
    enough for pKa estimates (see e.g. reviews by Warshel from 1991 and
    2006). I've never used H++ myself, only heard about it.<br>
    <br>
    Erik<br>
    <br>
    Monisha Hajra skrev 2011-03-29 17.31:
    <blockquote
      cite="mid:AANLkTinPguD9kg+KESgWuqooWmNYsNhEOnh_Czm1xUQP@mail.gmail.com"
      type="cite">Thanks Justin. I haven't find any such tutorial or
      exact relevant research paper. Find some paper though (<a
        moz-do-not-send="true"
        href="http://peds.oxfordjournals.org/content/16/12/1017.full.pdf+html">http://peds.oxfordjournals.org/content/16/12/1017.full.pdf+html</a>&nbsp;),
      not sure how they have done.<br>
      <br>
      <div class="gmail_quote">On Tue, Mar 29, 2011 at 8:51 PM, Justin
        A. Lemkul <span dir="ltr">&lt;<a moz-do-not-send="true"
            href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span>
        wrote:<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>
            Monisha Hajra wrote:<br>
            <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
              0.8ex; border-left: 1px solid rgb(204, 204, 204);
              padding-left: 1ex;">
              Friends,<br>
              <br>
              Need a Gromacs tutorial to find effect of pH on catalytic
              side. Any help?<br>
            </blockquote>
            <br>
          </div>
          There probably isn't one. &nbsp;If it isn't at <a
            moz-do-not-send="true"
            href="http://www.gromacs.org/Documentation/Tutorials"
            target="_blank">http://www.gromacs.org/Documentation/Tutorials</a>
          or you can't find it with Google, then it doesn't exist.<br>
          <br>
          You'll probably want to look into the ability of pdb2gmx to
          alter side chain protonation state, and otherwise base your
          procedures on published literature. You may need to use QM/MM
          rather than vanilla MD for this type of process, depending on
          your system and your goals.<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;">
            <br>
            Regards<br>
            <br>
            <br>
          </blockquote>
          <br>
          -- <br>
          ========================================<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 moz-do-not-send="true" href="http://vt.edu"
            target="_blank">vt.edu</a> | (540) 231-9080<br>
          <a moz-do-not-send="true"
            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>
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      <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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