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Dear Anthony,<br>
<br>
You can apply distance restraints to pairs of atoms, e.g. CA atoms in
your domains. Check the manual.<br>
<br>
Ran.<br>
<br>
Anthony Cruz wrote:
<blockquote cite="mid200804180922.53083.acb15885@uprm.edu" type="cite">
<meta name="qrichtext" content="1">
<p>On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote:</p>
<p>> Anthony Cruz wrote:</p>
<p>> > Hi User:</p>
<p>> > We have a protein with two domains. This two domains
were connected by</p>
<p>> > two linkers of different length. We want to study the
different</p>
<p>> > conformation that the protein domains can adopt
depending the length of</p>
<p>> > the linkers without loosing the secondary structure
feature present. I</p>
<p>> > was thinking in use some position restrain in the
backbone atoms of the</p>
<p>> > domains and leave the linkers and all the side chains to
move freely but</p>
<p>> > this aproach will not let the system to change the
conformation.</p>
<p>> > I'm using GROMACS 3.2.1.</p>
<p>> > With a dihedral constraint it will be posible to what I
want to do?</p>
<p>> > How can I do it?</p>
<p>> > There is any other option to do this?</p>
<p>></p>
<p>> This didn't get an answer earlier this week, probably because
of the way</p>
<p>> you've worded it. It's a bad idea to presuppose things about
the</p>
<p>> solution in your description, because if you're right then
people wonder</p>
<p>> why you are being lazy and not trying it out, and if you're
wrong then</p>
<p>> you're distracting people from identifying the real
solution... see</p>
<p>> <a class="moz-txt-link-freetext" href="http://catb.org/~esr/faqs/smart-questions.html#symptoms">http://catb.org/~esr/faqs/smart-questions.html#symptoms</a></p>
<p>></p>
<p>> You seem to want to let your domains move relative to each
other, but</p>
<p>> also to deny them much internal freedom. So what you want to
do is</p>
<p>> enforce (some of) their internal structure. Thus, use
distance restraints.</p>
<p>></p>
<p>> Mark</p>
<p>Thank you for your answer. But probably I don't make my point
clear. I have a protein with two units (domains). I think that distant
restraint will restraint the distance between the two domains or
units... This is done by the linkers between them. I want them to move
freely but not to change its structure, like freezing the backbone and
let the rest to move freely. </p>
<p><span style="font-weight: 600;">How I could do this?</span> </p>
<p>I think that I explain my problem better this time.</p>
<p>I presuppose things about the solution because I don't want that
the people in the mailing list think that I just have the problem and
not try to resolve it my self. Thank you for your advise Mark I will
try to change the way I make the questions. </p>
<p>Anthony</p>
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<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
------------------------------------------------------
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