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    On 24/02/2012 6:55 PM, James Starlight wrote:
    <blockquote
cite="mid:CAALQopzgE7w17y7Tq4M7gdFCHkr+kYWCeHrGv3qtMXUNAxEYRQ@mail.gmail.com"
      type="cite">Mark,<br>
      <br>
      what about the next sollution<br>
      <br>
      firstly I'll align both of my structures ( x-ray with water and
      another my model without water) <br>
      <br>
      than I'll copy aligned water from first structure to my model in
      the bottom of the GRO file.<br>
      <br>
      than I'll minimise this editted structure to relax side chains of
      the residues wich are in contact with the new waters<br>
      <br>
      Might this aproach be usefull? Commonly I use it to prepare
      protein-ligand complexes.<br>
    </blockquote>
    <br>
    Might work, but there are lots of steric issues and potential
    problems.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
cite="mid:CAALQopzgE7w17y7Tq4M7gdFCHkr+kYWCeHrGv3qtMXUNAxEYRQ@mail.gmail.com"
      type="cite">
      <br>
      James<br>
      <br>
      <div class="gmail_quote">2012/2/24 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><br>
        <blockquote class="gmail_quote" style="margin:0 0 0
          .8ex;border-left:1px #ccc solid;padding-left:1ex">
          <div text="#000000" bgcolor="#FFFFFF">
            <div class="im"> On 24/02/2012 6:31 PM, James Starlight
              wrote:
              <blockquote type="cite">Up! :)<br>
                <br>
                Please provide me with the best sollution of my problem!
                I just want to copy some water mollecules from X-ray
                structure to my model and place it in the identical
                possitions inside the TM budle of my protein.&nbsp; What are
                the most trivial way to solve this task?<br>
              </blockquote>
              <br>
            </div>
            You have a non-trivial problem. You can either build the
            model on the structure that has the waters (pdb2gmx doesn't
            strip water, IIRC), or work out some geometric criteria for
            placing the waters afterwards. Not every problem has an
            existing tool for its solution.<span class="HOEnZb"><font
                color="#888888"><br>
                <br>
                Mark</font></span>
            <div class="im"><br>
              <br>
              <blockquote type="cite"> <br>
                James<br>
                <br>
                <div class="gmail_quote">2012/2/22 James Starlight <span
                    dir="ltr">&lt;<a moz-do-not-send="true"
                      href="mailto:jmsstarlight@gmail.com"
                      target="_blank">jmsstarlight@gmail.com</a>&gt;</span><br>
                  <blockquote class="gmail_quote" style="margin:0 0 0
                    .8ex;border-left:1px #ccc solid;padding-left:1ex">
                    Dear Gromacs Users!<br>
                    <br>
                    I want to perform simulation of the membrane
                    receptor in the membtane environment. There are some
                    evidence about precense of the functional-relevant
                    internal water mollecules in the transmembrane
                    alpha-helix bundle of the receptor.<br>
                    <br>
                    <br>
                    I want to take into account that internal water in
                    my model. I have coordinates of the X-ray structures
                    wich have all that water. Also I have perfect model
                    of the same protein wich have not that water but
                    have full-length structure ( there are some missing
                    residues in the X-ray structures- e.g in the loop
                    regions).<br>
                    <br>
                    So what the best way to build system would&nbsp; be in my
                    case?<br>
                    <br>
                    1-&nbsp; Should I use X-ray structure where internal
                    water has already present and build missing loops
                    via model software ? How I could preserve the
                    internal waters in that starting structure when this
                    structure will be processed by pdb2gmx ?<br>
                    <br>
                    2- Or the best way is to incorporate all waters in
                    the model of my protein ? If this aproach could be
                    better what is the simplest way to transfer exact
                    coordinates of water in that holo model ? )<br>
                    <br>
                    Thanks for help<span><font color="#888888"><br>
                        <br>
                        <br>
                        James<br>
                      </font></span></blockquote>
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          --<br>
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