AMBER Archive (2006)

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

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Wed Nov 15 2006 - 18:30:48 CST

Dear Ilyas,

in case you can use explicit solvent MD, I would
not go for implicint solvent simulation. Yes, it increases
sampling, but it also adds numerous additional uncertainties
and approximations. Significant ones. What parameters do you use for your
implicit model? You may wish for example to test sensitivity
of the results to atomic radii, it would show you the
sensitivity of the method to paramaters.
It is unfortunately common to all continuum solvent approaches
(including the QM ones like PCM, COSMO etc).

Best wishes, Jiri

> 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/ -
> > > ---------------------------------------------------------------
> > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
>
> --
> 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/ -
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu