Hi,<div><br></div><div>This query is related to my previous queries. I want to constraint the psi/psi angle of the turn residue of my beta-hairpin , meaning that they are allowed to move in certain range of psi/phi angle space. Simultaneously, I want to freeze the movement of strand residues. This procedure has to be followed during minimization alone. From the previous answers to my queries I understood how to constrain dihedral space, but I don't know how to fix the movement of strand residues ?? ... any help will be highly appreciated. <br>
<br><div class="gmail_quote">On Thu, Jun 14, 2012 at 4:24 PM, bharat gupta <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Sorry for the last reply, I wrote turns with different sequences wrongly, it'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 ??<div class="HOEnZb">
<div class="h5"><br>
<br><div class="gmail_quote">On Thu, Jun 14, 2012 at 4:16 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>
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't compare total energies of different sequences and get a
meaningful answer. What'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't necessarily relate to the same quantity measured for an
orange, either. There's a lot of work in measuring a decent *free*
energy difference between some states.<div><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 "constraints" and
"restraints" 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't measure anything relevant.<div><div><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"><<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> 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"><<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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