[gmx-users] Conformation search!

[Ran Friedman]

Dear Anthony,

You can apply distance restraints to pairs of atoms, e.g. CA atoms in
your domains. Check the manual.

Ran.

Anthony Cruz wrote:
>
> 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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-- 
------------------------------------------------------
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: r.friedman at bioc.unizh.ch
Skype: ran.friedman
------------------------------------------------------

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