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

[olivier walker]

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

thanks

olivier




**************************************************
Olivier WALKER
Department of Chemistry & Biochemistry
University of Maryland
College Park, MD 20742
USA
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Fax : 301-314-0386
Phone : 301-405-8710
E-mail : oliwalk at wam.umd.edu
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