AMBER Archive (2006)

Subject: AMBER: AMBER minimization vs. Gaussian optimization

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Oct 04 2006 - 15:27:48 CDT

Dear All,

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
structures which are close to the gaussian optimized structures - 3' endo
(rmsd < 0.2 for modified residues, while rmsd > 1 for unmodified residues,
compared to the optimized gaussian structures).

I will appreciate if anyone can give me any kind of explanation on this (I
am pretty confused). Thanks in advance.

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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