AMBER Archive (2006)

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

From: FyD (fyd_at_u-picardie.fr)
Date: Thu Oct 05 2006 - 00:14:07 CDT

> 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?
> 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

You could look at R.E.DD.B. for projects containing regular DNA & RNA
nucleotides.
See among many other projects:
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/ for DNA
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-51/ for RNA
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-60/ for DNA & RNA

Download the corresponding .tar.bz files, the PDB files are HF/6-31G*
optimized structures of C3'endo conformation for RNA and C2'endo &
C3'endo conformations for DNA.

They could be good starting point for your own QM optimization structures...
Description of the use of QM constraints during the optimization step
is also provided...

regards, Francois

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