AMBER Archive (2006)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Nov 15 2006 - 18:05:13 CST

Dear Jiri,

Thanks for your quick response. I have done a 65 ns explicit solvent sim.
for the iGiGiCiC helix, and it still stays the same. This is a nice result
to see that the force field is not causing the problem in implicit
solvent. The reason why I want to use implicit solvent in my project is to
do sampling better. Explicit solvent case is working fine, but the
computation time is too much. The residues G and C are not too different
compared to iG and iC: G-C and iG-iC base pairs have 3 h-bonds; the resp
charges do not differ too much either. I am wondering how I can mimic the
GGCC implicit solvent simulation with iGiGiCiC implicit solvent
simulation. Thanks.

Best,

On Thu, 16 Nov 2006, Jiri Sponer wrote:

> 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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-- 
  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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