On Wed, Jul 27, 2011, Brian Radak wrote:
>
> I'd like to apply a half harmonic restraint to a dihedral angle, but I'm not
> exactly sure how to do this since the angle is obviously periodic. That is,
> I'd like there to be a harmonic wall if the well minimum (say 25 for sake of
> argument) is approached from one end (e.g. when it was previously 30), but
> there to be no restraint far from this value (e.g. at +170 or -160 say,
> there would be no restraint).
There is no general way to do this (in Amber) if the dihedral angle is really
visiting all possible angles. For your example, r1 = -190, r2=25, r3=25,
r4=50, rk2=0., rk3=nonzero will work if the angle is not too far away from
the target of 25.
...dac
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Received on Thu Jul 28 2011 - 08:00:04 PDT
