AMBER Archive (2009)

Subject: [AMBER] partial charge and topology of intrastrand cross-link DNA

From: Shuang Ding (
Date: Mon May 25 2009 - 21:27:43 CDT

Hi all,

I try to perform MD simulations of 11mer DNA duplexes which have (1,2) or (1,3) intrastrand cross-links. One of the modified base formed bonds directly with nearby base.
How should I calculate the partial charges of the cross-links and define the topology of them?

Any suggestion is appreciated. Many thanks!

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