Re: AMBER: torsional restraints in a solvated MD simulation.

From: David A. Case <>
Date: Tue, 14 Aug 2007 13:50:31 -0700

On Tue, Aug 14, 2007, Tom Pochapsky wrote:

> I am trying to force a cis -> trans isomerization of a peptide bond
> during a standard solvated MD simulation using Amber 8. I have
> included a standard torsion restraint file to be applied gradually
> during the simulation, but cannot detect any change; furthermore, no
> torsional energies are reported in md.out ,

Set pencut to a negative number, if you want to be sure the potential is being

> > &rst iat = 1321, 1336, 1338, 1348,
> > r1 = -531.0, r2 = -530.0, r3 = -180.0, r4 = -179.0,
> > rk2 = 100.0, rk3 = 100.0, &end

This is certainly a weird constraint! Because dihedral angles are circular,
Amber adds or subtracts 360 degrees from the current angle to get it as close
as possible to the center of the flat region, then applies the restraint.

In your case, an initial "cis" angle near 0 degrees would be converted to -360
degrees (close the midpoint between -530 and -180). The program would then
decide that no penalty should be applied (since the current angle is between
r2 and r3).

Why not set r2 to 170 and r3 to 190 if you want to force the angle to become
trans? I'd also suggest lowering rk2 and rk3, but you may want to experiment
with that.


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Received on Wed Aug 15 2007 - 06:07:56 PDT
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