[Chimera-users] force field for G-quadruplexes

[Gilmar Salgado]

Hello,
recently I was looking into the capabilities of Chimera minimization tools
to minimize the structure of a DNA G-quadruplex molecule.
The problem is that all G-quadruplexes have an ion (K+ or Na+) in-between
and stabilizing the tetrads. I wonder if the force field available in
chimera are "decent" to water-minimize this kind of structures? ...and
which one is more adapted, after all those are non-conventional DNA
structures.
Thanks in advance for your input

Gilmar Salgado

Université Segalen
Laboratoire ARNA (INSERM U869)
Institut Européen de Chimie et Biologie
2 rue Robert Escarpit
33 076 Pessac Cedex
FRANCE
+33(0) 540 0022 24
+33(0) 557 571 015 (fax)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130704/4abbaef6/attachment.html>