Dear all,
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.
I hope you can help me on an advice on how to proceed. In particular,
is rigid body dynamics as part of cartesian coord annealing possible
using the python interface?
best regards,
Jakob
--
Jakob Toudahl Nielsen, post doc
Laboratory for Biomolecular NMR Spectroscopy
inSPIN, Center for Insoluble Protein Structures
Department of Chemistry, University of Aarhus
Langelandsgade 140, DK-8000 Aarhus C, Denmark
Phone: +458942 5528 or +452993 8502 (cell)
