AMBER Archive (2005)

Subject: AMBER: DNA base-flipping: TI vs PMF

From: Lauren O'Neil (lhunter2_at_nd.edu)
Date: Tue May 31 2005 - 10:40:45 CDT

    I would like to calculate the free energy change for the process of
base-flipping in DNA using Amber. I have been working with the online
tutorial of thermodynamic integration in Amber and have a few questions
as to how I could implement this for the base-flipping of damaged DNA.
   Along the lines of the tutorial I was thinking of a cycle in which
DNA (flipped-in)-->water and DNA (flipped-out)--> water using dummy
atoms. Can Amber handle using that many dummy atoms (DNA = duplex
16-mer)? How could I ensure that the two "water" states are the same,
or can I? To get around the waters being the same I was also thinking
of starting with a water box that contained both the flipped-in and
flipped-out DNA (as dummy atoms) and then going both the flipped-in and
flipped-out directions to get the free energy difference. The larger
question is - How do you determine that the reference state (water) is
the same for any cycle? Also, could this be done directly (without a
common reference state)? If yes, can Amber do this?
  I am interested in using thermodynamic integration rather than
potential of mean force for this calculation because of the choice of
path for the flipping process. Any thoughts??
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