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. 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.... <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 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>
</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 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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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <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>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>
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