AMBER Archive (2006)

Subject: Re: AMBER: question capping helix ends

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Fri Mar 24 2006 - 03:09:11 CST

Hi Zuang,
   
  I have had a similar experience with an RNA system which has a 5bp A-RNA stem region (mainly G:::C bp ) capped with a 5nt and a 7nt RNA fragments from each end. After a 300 ps MD in explicit water at 300 K and MM-PBSA computations for 100 snapshots between 150 ps and 300 ps, it turned out that my RNA system was energetically not as stable due to high electrostatic and van der Waals energy violations. Also the G:::C bps at the ends of the RNA helix tends to unwind. Later I pruned the 5nt cap from one end to yield an RNA hairpin and rerun MM-PBSA. Then I found out that the electrostatic tension over the new RNA hairpin system was considerably reduced resulting in a more stable structure.
   
  Hope this helps you in designing your DNA system.
   
  best regards,
   
  jenk.
   
   
       

Zhuang <ezhuang_at_chem.ucsb.edu> wrote:
  Thanks for the reply. I suppose the ends are probably ok if I run my
simulation at 300K room temperature. But I'm hoping to run it at
higher temperature in explicit water and I'm worried the ends will fly
apart at high temperature.

                
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