Subject: DNA Base-Flipping: TI vs PMF

From: "Lauren O'Neil" <lhunter2 (a) nd.edu>
Date: Tue, 31 May 2005 10:50:19 -0500

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??

Lauren L O'Neil
lhunter2 (a) nd.edu