From parisien@iro.umontreal.ca
Date: Mon, 10 May 2004 11:28:18 -0400 (EDT)
From: Marc Parisien <parisien@iro.umontreal.ca>
Cc: xiangjun@rutchem.rutgers.edu, songliu@buffalo.edu
Subject: DNA deformation energy!


Hi All!

	I have received the mean values from Dr. Lankas;

        Lankas F, Sponer J, Langowski J, Cheatham TE 3rd.
          DNA deformability at the base pair level.
          J Am Chem Soc. 2004 Apr 7;126(13):4124-5.

	We now have the base-pair level deformation energies!!
	I have updated the program; see attached files :-)


	I have decoupled the energy calcs since there is the possibility 
of coupled interactions between base-pairs and base-steps parameters...
(like Propeller-Rise, etc)   another article maybe for that ;-)
It would generate a huge matrix though: 12 x 12  (6 params for bases + 6 
params for steps = 12 total params).

	I have also change the energy calcs loops from:

	1)
	i = 0 to 5  // the 6 parameters
	j = 0 to 5

	to

	2)
	i = 0 to 5
	j = i to 5

	because in 1) the i-j and j-i are counted twice, except for i-i,
	so it is not correct to then simply divide by 2.
	in 2) the i-j are counted singly, even for i-i.

	Regards,
	Marc.

//--------------------------------------------
Marc Parisien
parisien@iro.umontreal.ca
www-lbit.iro.umontreal.ca

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