AMBER Archive (2003)

Subject: RE: AMBER: infinitely long DNA & moil-view?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Oct 14 2003 - 15:36:56 CDT

> 1) You have to know the periodicity of your DNA (how many bp per turn)
> and choose the one that exactly matches complete turns (13 bp, as I
> recall).

(Different for A and B conformations.)

> 2) Construct it and manually modify the end residues and connect the
> ends. You'd need to define your own residues, for instance.

I think the standard non-terminal residues would work (DG, DA, DC, DT).

Bill Ross

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