[Chimera-users] force field for G-quadruplexes

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 5 09:25:52 PDT 2013


Hi Gilmar,
The general recommendation is to use the current default in Chimera (AMBER ff12SB) but I don't have any specific knowledge of how it performs on nucleic acids or quadruplexes.

We aren't in the force field development business ourselves, so all I can suggest is to look at the AMBER documentation, including published papers that describe the different versions of the force fields and how they were validated. Some papers are cited in the Chimera manual,
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html#standard>
...more information in the AMBER manual and at the AMBER website: http://ambermd.org/

You could also ask on the AMBER mailing list, but I believe you have to join the list to send mail to it.
<http://ambermd.org/#reflector>

A final issue is that in general, minimization has limited ability to significantly change coordinates from the starting structure.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 4, 2013, at 12:56 AM, Gilmar Salgado wrote:

> 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




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