Sorry for the last reply, I wrote turns with different sequences wrongly, it&#39;s actually the turn with different dihedral constraints. I searched the gromacs user list , where I found this link , regarding calculation of dihedral energy of selected residues.  I want to know whether this method would be useful ??<br>
<br><div class="gmail_quote">On Thu, Jun 14, 2012 at 4:16 PM, Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

  
    
  
  <div bgcolor="#FFFFFF" text="#000000"><div class="im">
    On 14/06/2012 4:57 PM, bharat gupta wrote:
    <blockquote type="cite">I am not going to compare this with anything , I have
      to look for sequences and their corresponding energies and select
      the lowest scoring ones.</blockquote>
    <br></div>
    You can&#39;t compare total energies of different sequences and get a
    meaningful answer. What&#39;s the difference in energy between an apple
    and an orange mean? You can compare the average energy of an apple
    cut into pieces with the average energy of a whole apple, but that
    doesn&#39;t necessarily relate to the same quantity measured for an
    orange, either. There&#39;s a lot of work in measuring a decent *free*
    energy difference between some states.<div class="im"><br>
    <br>
    <blockquote type="cite"> I request you to kindly elaborate on freezing some
      portion of the protein. ( I am bit confused as in my case I am
      fixing the dihedral of turn residues which means constraining them
      simultaneously I want to freeze the other region of the protein. )</blockquote>
    <br></div>
    You need to read the link I gave last time and use &quot;constraints&quot; and
    &quot;restraints&quot; in the accepted GROMACS sense in order for people to be
    able to understand your meaning clearly. There are links there to
    the kind of methods that are available. I think you need to do some
    reading and thinking about those :-) If you lock down all the
    degrees of freedom then you can&#39;t measure anything relevant.<div><div class="h5"><br>
    <br>
    Mark<br>
    <br>
    <blockquote type="cite">
      <div>
        <br>
        <br>
        <div class="gmail_quote">On Thu, Jun 14, 2012 at 3:50 PM, Mark
          Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div bgcolor="#FFFFFF" text="#000000">
              <div> On 14/06/2012 4:38 PM, bharat gupta
                wrote:
                <blockquote type="cite">Thanks Sir for the reply... This
                  question is related to my first query that if we
                  constraint the dihedral of the turn residue how can we
                  fix/freeze the movement of other residues.</blockquote>
                <br>
              </div>
              <a href="http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints" target="_blank">http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints</a>
              <div><br>
                <br>
                <blockquote type="cite"> As I am interested in only
                  getting the energy of the hairpin when the turn
                  residues are constrained within a particular phi psi
                  angle range.... <br>
                </blockquote>
                <br>
              </div>
              .. and with what are you going to compare those energies?
              And what will that comparison mean?<span><font color="#888888"><br>
                  <br>
                  Mark</font></span>
              <div>
                <div><br>
                  <br>
                  <blockquote type="cite">
                    <div> <br>
                    </div>
                    <div><br>
                      <div class="gmail_quote">On Thu, Jun 14, 2012 at
                        11:21 AM, Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span>
                        wrote:<br>
                        <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                          <div>On 14/06/2012 12:04 PM, bharat gupta
                            wrote:<br>
                            <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Thanks for
                              the reply . Is it possible to calculate
                              the dihedral energy of certain residues,
                              like in my case for turn residues ??.. How
                              can that be done<br>
                            </blockquote>
                            <br>
                          </div>
                          First, seek to define &quot;dihedral energy&quot;...
                          Force fields are not parametrized such that
                          parts of them are expected to correlate with
                          observables.
                          <div><br>
                            <br>
                            <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br>
                              This another question is regarding energy
                              minimization. Suppose, I minimize the the
                              protein solvated in water, the energy
                              value that I get is for the whole system
                              or for the protein alone. If it&#39;s for the
                              system then how can I get the energy for
                              the protein alone.<br>
                            </blockquote>
                            <br>
                          </div>
                          You can define energy groups (see manual) to
                          do this for the nonbonded contributions.
                          Bonded contributions are easy to do in your
                          case. Whether this energy is useful for
                          anything is quite another matter.<span><font color="#888888"><br>
                              <br>
                              Mark</font></span>
                          <div>
                            <div><br>
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                      Bharat<br>
                      Ph.D. Candidate<br>
                      Room No. : 7202A, 2nd Floor<br>
                      Biomolecular Engineering Laboratory<br>
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        Bharat<br>
        Ph.D. Candidate<br>
        Room No. : 7202A, 2nd Floor<br>
        Biomolecular Engineering Laboratory<br>
        Division of Chemical Engineering and Polymer Science<br>
        Pusan National University<br>
        Busan -609735<br>
        South Korea<br>
        Lab phone no. - +82-51-510-3680, +82-51-583-8343
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          Mobile no. - 010-5818-3680<br>
          E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
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Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>
Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>