Hello Yikan--
>
> I want to do the rigid body conformational sampling using the dock2.py in the
> attachment.
> but, 1) I found that all of the 5 domains do not rotate randomly and freely,
> instead just rotate or translate around the center of mass. Then the sampling
> may not search the conformational space enough.
randomizeDomainPos should rotate the segments uniformly randomly, and
in the distance range +/-80 angstrom of their starting
position. However, the first minimization utilizes the bond term which
will bring them back together along with the linker segments- this
will tend to place the structures back close to where they started
from.
> 2) I do not know how to edit the scripts to let the 5 domains move
> randomly and freely. Do they can be effected with “randomizeDomainPos”?
I suspect it's fine. However, if you're not satisfied with the current
sampling, you might first try fixing the randomized domain positions
and allowing only linkers to move during initial minimization. Also, I
suggest that you write out a PDB after each stage which you're not
certain about. For instance, you might add this at line 245:
protocol.writePDB('init_%d.pdb'% loopInfo.structNum)
and see if you're happy with the sampling.
best regards--
Charles
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