[gmx-users] bond angle constraints

[jxs818 at bham.ac.uk]

Hi all, 
I am a bit stuck. I have a protein in a ground/unactivated 
state and I also have some distance restraints from spin 
labelling with a ligand bound. I think that the overall 
secondary structure in my protein is maintained but there 
is some movement of helices etc. Can I break my protein 
down into its component secondary structural elements, then 
add constraints = all-angles (keeping these secondary 
structural elements as rigid bodies ?), then finally add 
distance restraints to parts of my protein to mimic a 
translation from the ground state to the ligand bound state.
This is probally really not right, has anyone else had a 
similiar problem??
As always any help is gratefully accepted.
John