Re: [Avogadro-Discuss] Double stranded DNA

[Geoffrey H. <ge...@pi...>]

On May 28, 2010, at 9:39 AM, Philip Rhoades wrote:

> The strands are close to each other but not in the correct, double 
> stranded position - I thought I would be able to "make" the hydrogen 
> bonds somehow and then click on "Optimize Geometry" which would drag the 
> strands into the correct position . .


If you are using MMFF94, it will recognize hydrogen bonds without any work on your part. Whether that will be enough to "zipper" a double strand, I don't know. You could also specify some constraints to enforce specific distances between pairs of atoms.

Hope that helps,
-Geoff

---
Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh
http://hutchison.chem.pitt.edu/
Office: (412) 648-0492