AMBER: Quantifying DNA perterbation

From: Kara Di Giorgio <>
Date: Tue, 15 Nov 2005 17:44:03 -0800

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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Received on Wed Nov 16 2005 - 01:53:00 PST
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