Dear All,
I have a system which is formed by unnatural base pairs; it is a
(5'iGiGiCiC3')_2 helix. This helix is more stable than (5'GGCC3')_2
structure. This is experimentally verified.
When I use implicit solvent model to simulate both these structures, GGCC
stays helical while iGiGiCiC falls apart.
Amber force field does not have an explicit term for H-bonds in the
potential energy function. In the old amber force fields, there is an
explicit H-bond term present in the function. I wonder why the H-bond term
is taken away from the force field, and how the 'H-bond' term is
incorporated into the new amber force field. This might help me to figure
out why iGiGiCiC is falling apart and how I can solve this problem. Thanks
in advance for any suggestions.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Nov 19 2006 - 06:07:13 PST
