AMBER Archive (2007)

Subject: Re: AMBER: Holding NA Base syn during annealing

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 22 2007 - 09:41:30 CST

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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu