[gmx-users] conformational study of a dual domain protein

[K.A. Feenstra]

David wrote:
> 
> On Fri, 2002-09-27 at 23:40, olivier walker wrote:
> >
> >
> > Hi all,
> >
> > Thanks to David for his answer in the CCL mailing list.
> >   I'm studying a dual domain protein and I would like to generate all
> > possible conformations according to some restraints.
> > Basically, I want to study all possible conformation of the link between
> > the two domains (8 residues) and freeze the two domains (not completely
> > because I would like to follow the shift of the domains with the
> > conformation change of the link).
> >
> > the main goal is to monitor the distance between two residues (located in
> > two different domain) when the conformation of the link is changing.
> >
> >
> > In such a case, I can't use dyndom because I've only one pdb file. I tried
> > to define an index file to specify a frozen group of atoms (typically the
> > link is free and the two domains are frozen) but I want the two domains to
> > move with reorientation of the link (like two balls attached by a rope).
> >
> > I'm sure this is possible to do in gromacs but I'm not comfortable enough
> > with this program to find the right way to do so immediately.
> >
> > has anybody experienced such a problem?  Any help is welcome
> This is not trivial. You probably realize you cannot study *all*
> conformations... You could probably generate some from the original pdb
> file using pymol by rotating a few torsions, then do short simulations
> and throw everything together in an essential dynamics analysis...
> Most important is that you ask yourself the question what you want to
> get out of it....

Couldn't concoord (written by Bert de Groot) do something in this respect?
I know it is good at creating a multitude of sensible possible conformations.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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