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Hello Simon--
> I have just started learning/using xplor and I am attempting to perform
> some simulated annealing, but to define a hinge at one end a helix to
> see what the potential movements are. At present I do not have any NMR
> restraints, but I would like know if this is possible both with or
> without NMR restraints. I have looked at the anneal.py script released
> with xplor, but I can't work out how to define a hinge at a specific
> place and then allow the simulation to just run.
>
Do you wish to freeze some secondary structure elements, and then allow
linking loop/turn regions to move? If so, use the IVM's group function
to group atoms in rigid bodies and then protocol.torsionTopology to use
torsion angle degrees of freedom for the remainder. For instance, from
eginput/gb1_rdc/anneal.py use the following ivm setup:
from ivm import IVM
dyn = IVM()
dyn.group("resid 11:20") # resids 11-20 and 40-50 will move as rigid bodies.
dyn.group("resid 40:50")
protocol.torsionTopology(dyn)
best regards--
Charles
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