On Wed, Aug 28, 2013 at 9:51 PM, Rodrigo Salazar <rodrigo.foton.gmail.com>wrote:
> Hi,
>
> I'm calculating a DNA doble strand fragment. The fragment consists in two
> complementary secuences: Adenine-Timine with Timine-Adenine. The problem is
> that the result is no symmetric when measuring its torsion angles and
> distances.
>
> Is there an option in amber to requiere symmetry?
>
No. Most biomolecules have C1 symmetry, and even those that have symmetry
in a crystal structure often lose that symmetry when subjected to
minimization or dynamics.
Also, unlike electronic structure calculations which can be _greatly_
simplified using symmetry if it exists, molecular mechanics calculations
benefit very little from such constraints.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 29 2013 - 05:00:04 PDT
