AMBER Archive (2006)

Subject: AMBER: H-Bond Terms in amber force field

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Nov 15 2006 - 13:28:06 CST

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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