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<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>> http://catb.org/~esr/faqs/smart-questions.html#symptoms</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></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></p>
<p>I think that I explain my problem better this time.</p>
<p></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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