On Thu, Mar 22, 2007, Seth Lilavivat wrote:
>
> Any advice on trying to keep a NA base in the syn conformation (like Z-DNA)
> while still being hydrogen bonded to its base pair during annealing? Right
> now I'm starting with it in the syn conformation and have a torsion
> restraint of 90 to 270 degrees with a force constant of 200 kcal/mol.
> During the annealing run it still pops back to the anti conformation.
I think you need to specify exactly what you mean by "torsion
restraint of 90 to 270 degrees with a force constant of 200 kcal/mol"
If you haven't already done so, plot that restraint you are using as a
function of the torsion angle. Make sure that the penalty for going to an
anti conformation is significant -- I would guess 10 kcal/mol or more is
needed for a simulated annealing, but the general idea is that you want to use
the smallest value you can get away with.
...good luck...dac
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Received on Sun Mar 25 2007 - 06:07:27 PDT
