On Thu, Feb 12, 2015, Urszula Uciechowska wrote:
>
> I was wondering if its possible to build a ssDNA in hairpin conformation
> using nab? Does anyone know other software where I could do this?
It is certainly *possible*: the pseudoknot example could be adapted to a
hairpin. It uses distance geometry to construct conformations satisfying
certain restraints, such as WC pairing in the stem.
Having said that, there are lots of other solutions, and a Google search will
point to many of them. I personally would use CYANA for this purpose, but
that is largely because I'm familiar with that code. You could also set up
constraints in sander and "fold" the dna from an extended configuration.
Maybe others on the list will have more specific suggestions.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 12 2015 - 04:30:02 PST
