AMBER Archive (2005)

Subject: AMBER: Quantifying DNA perterbation

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Tue Nov 15 2005 - 19:44:03 CST

Does anyone know of a method to quantify how much DNA has been
perterbed during a MD run? I have done MD simulations of DNA with a
cross-linker of various lengths in it. I need to compare how much each
linker perterbed the DNA. Does anyone have any ideas?

Thank you,

Kara Di Giorgio

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