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Hello Jakob--
> I would like to perform a rigid body optimization of an oliomeric
> structure using only sparse ambiguous intermolecular "NOEs" and
> different symmetry-restraints. My molecular is a homo-pentamer. I have
> tried using the python interface using the IVM module as in
> eginput/gb1_rdc/anneal.py:
>
> ...
> dyn.group(AtomSel('segid A'))
> dyn.group(AtomSel('segid B')) #and so on with C, D, and E
> ...
>
> However, this approach does not seem to have the desired effect, the
> structures fail to converge. I appears to me that IVM is not the best
> choice since I have no free parts in the molecule, first I hoped that
> the remaining degrees of freedome in the translation and rotation of
> the monomers would do the trick, but it seems not... Actually it seems
> like its only the final cartesean coord minim that helps.
> I tried using the old interface and "dynamics rigid" rather than
> "dynamics internal". This works better, but I would prefer using the
> python interface.
>
The group statements will hold the subunits rigid, and should allow them
to move as rigid bodies. Is this what you desire? Of course you will
also need symmetry restraints (distance symmetry if the subunits are
moved as rigid bodies). From your description I'm not certain what the
nature of the problem is.
best regards--
Charles
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