[gmx-users] Conformation search!

[Mark Abraham]

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