AMBER Archive (2006)

Subject: AMBER: DNA helix end stable?

From: a a (patd_2_at_hotmail.com)
Date: Tue Nov 28 2006 - 21:35:11 CST

Dear Sir/Madam,

I am trying to do MD for DNA, I noted that the end of the DNA helix is very
flexible (the double helix structure is lost too). Is it well known that
double helix structure of DNA end will be unstable? I did the calculations
with implicit solvent, but I found some other publications indicate the same
observations when they used explicit solvent instead. Is it normal or just
that I should change the conditions for the calculations to correct this
problem?

Best regards,

Annie

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