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. 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. )<div>
<br><br><div class="gmail_quote">On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham <span dir="ltr"><<a 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 bgcolor="#FFFFFF" text="#000000"><div class="im">
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 class="im"><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 class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><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"><<a 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>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 "dihedral energy"... 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'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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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>
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