AMBER Archive (2006)

Subject: Re: AMBER: AMBER minimization vs. Gaussian optimization

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Oct 04 2006 - 17:17:51 CDT

Thanks for the quick response and the paper Tom.

Best,

On Wed, 4 Oct 2006, Thomas Cheatham wrote:

>
> > I have a question regarding the sugar pucker of the nucleic acid residues.
> > For watson-crick bases (nucleosides), the gaussian optimized structures
> > are in 3'-endo conformation while the AMBER minimized structures are in
> > 2'-endo conformation. Is the AMBER force field parameters choosen such
> > that the nucleic acid residues are forced to have 2'-endo character?
>
> I think that minima should be present at both C3'-endo and C2'-endo
> (although they may be shifted a bit) for both AMBER and Gaussian and will
> be different for ff94, ff98 and ff99 in AMBER.
>
> What local minima is found will depend on the starting structure (and
> environment). In practice, with ff94 in DNA, C3'-endo is only a transient
> state (not clear if it is a minima during solvated dynamics) whereas with
> ff99, distinct C3'-endo and C2'-endo populations are found. With RNA,
> C3'-endo and C2'-endo puckers are minima.
>
> So, I do not understand that gaussian finds 3'-endo and "AMBER" 2'-endo
> except that minimization from a given structure can go anyway. One way to
> force the pucker state is to restrain delta during the initial
> minimization (as per what I did a long time ago in "How sensitive are
> the results ..." paper in the proceedings of the 10th converstation paper at:
> http://www.chpc.utah.edu/~cheatham/protected/publications/how_sensitive_jbsd.pdf
> (username: steroid, password: steroid)
>
> There I restrained C1'-C2'-C3'-C4' to between 30-40 deg for C3'-endo and
> to between -38 to -40 for C2'-endo.
>
> > For my modified nucleic acid residues, when I minimize them using AMBER
> > force field, I am not getting the 2'-endo character. I am getting
>
> I think you will have to force it to repucker during the minimization; try
> using the restaints as outlined above initially...
>
> --tom
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> 

-- 
  Ilyas Yildirim
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