

In theory, you could do a perturbation of one residue to
another; AMBER's free energy program does this. Since
sampling is a big issue, there is a bit of art in doing
this, so I'd advise reading papers on it.. no refs handy.
the good news is that AMBER is pretty cheap, and the next
release which is due 'any week' will have some graphics
for setting up the molecule files. See 

  http://www.amber.ucsf.edu

Bill Ross
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