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On 14/06/2012 4:38 PM, bharat gupta wrote:
<blockquote
cite="mid:CAAh+zSUTvqqxatuTXhm1b2uz8pcJLf62vcNmY7HqfaeaWnAe-A@mail.gmail.com"
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>
<a
href="http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints">http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints</a><br>
<br>
<blockquote
cite="mid:CAAh+zSUTvqqxatuTXhm1b2uz8pcJLf62vcNmY7HqfaeaWnAe-A@mail.gmail.com"
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>
.. and with what are you going to compare those energies? And what
will that comparison mean?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAh+zSUTvqqxatuTXhm1b2uz8pcJLf62vcNmY7HqfaeaWnAe-A@mail.gmail.com"
type="cite">
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<div class="gmail_quote">On Thu, Jun 14, 2012 at 11:21 AM, 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>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">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>
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First, seek to define "dihedral energy"... Force fields are
not parametrized such that parts of them are expected to
correlate with observables.
<div class="im"><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's for the system then how
can I get the energy for the protein alone.<br>
</blockquote>
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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 class="HOEnZb"><font
color="#888888"><br>
<br>
Mark</font></span>
<div class="HOEnZb">
<div class="h5"><br>
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-- <br>
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>
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South Korea<br>
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