David A. Case wrote:
> 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
> applied.
>
>>> &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.
>
Oops. I generated this from a five-column DYANA type restraint file,
but it is possible that since I specified -185 degrees, and the lower
limit to be -175, this happened. I will try your suggestion and let you
know how it works.
Thanks, Tom
> 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.
>
> ....dac
>
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Received on Wed Aug 15 2007 - 06:07:59 PDT
