[gmx-users] Conformation search!

[Anthony Cruz]

On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote:
> Anthony Cruz wrote:
> > Hi User:
> > We have a protein with two domains. This two domains were connected by
> > two linkers of different length. We want to study the different
> > conformation that the protein domains can adopt depending the length of
> > the linkers without loosing the secondary structure feature present. I
> > was thinking in use some position restrain in the backbone atoms of the
> > domains  and leave the linkers and all the side chains to move freely but
> > this aproach will not let the system to change the conformation.
> > I'm using GROMACS 3.2.1.
> > With a dihedral constraint it will be posible to what I want to do?
> > How can I do it?
> > There is any other option to do this?
>
> This didn't get an answer earlier this week, probably because of the way
> you've worded it. It's a bad idea to presuppose things about the
> solution in your description, because if you're right then people wonder
> why you are being lazy and not trying it out, and if you're wrong then
> you're distracting people from identifying the real solution... see
> http://catb.org/~esr/faqs/smart-questions.html#symptoms
>
> You seem to want to let your domains move relative to each other, but
> also to deny them much internal freedom. So what you want to do is
> enforce (some of) their internal structure. Thus, use distance restraints.
>
> Mark

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. 
How I could do this? 

I think that I explain my problem better this time.

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. 
Anthony
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