AMBER Archive (2005)

Subject: Re: AMBER: Adding residues to a DNA sequence

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 25 2005 - 16:39:23 CDT

On Sun, Jul 24, 2005, Kara Di Giorgio wrote:

> I have a piece of DNA from the protein data base and I'd like to extend
> the ends by two residues. Does anyone have any idea how to easily do
> this?
>

Build a regular helix with the sequence you want, that partially overlaps
the two residues in the database file. Then superimpose the atoms of the two
residues in the database file with those of the regular helix. That will
orient the regular helix in the right way. Then you can replace the two
residues in the database file with the (longer) regular helix. You will
probably need some minimization to make sure that there is no strain at the
interface region.

...good luck....dac

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