Dear Ilyas:
the problem most likely comes from the implicit model.
(Stability of your GGCC with implicit model does not mean
that it is correct in all aspects, it just does not fall
appart in your particular simulation).
You need to be exceptionally careful with implicit models
and do not expect high accuracy, there are numerous fundamental
approximations.
Explicit H-bond term to the best of my knowledge is not needed
and amber, when charges are consistently derived, match
close to perfectly MP2 complete basis set + CCSD(T) correction
data for stacking and base pairing unless bases are formally
protonated.
There obviously are molecular orbital contributions to H-bonding
and stacking not included in forcefields but these do not
cause major troubles in standard simulations and would not be included
via the old H-bond term.
(Actually, if this is H-bond error, it would fall appart
with explicit solvent, too).
Best wishes Jiri
> 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 - 06:07:15 PST
