[gmx-users] Conformation search!
Mark.Abraham at anu.edu.au
Fri Apr 18 03:13:31 CEST 2008
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
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.
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