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
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- 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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Received on Sun Oct 08 2006 - 06:07:10 PDT
