AMBER Archive (2006)

Subject: Re: AMBER: Creating an Intercalation site

From: Bill Ross (
Date: Mon Jul 17 2006 - 14:49:20 CDT

> Can someone please suggest to me the best software / method in going
> about creating an intercalation site... for example intercalalting
> RNA/DNA with a small molecule?

I believe there's an older paper on ethidium intercalation by
Lybrand that gives backbone torsion angles. It is tedious but
doable to apply these in a molecule editor. It might be possible
and easier to apply them as restraints.

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