Re: [AMBER] Extending DNA structure

From: Vlad Cojocaru <>
Date: Tue, 19 Jan 2021 10:39:58 +0100

We usually use NAB to create the extension in the needed conformation
adding 1-2 bases (base pairs) common between the extensions and the
structure. Then, using VMD we superimpose the extensions on the
structure using the common part. Then, again in VMD we process the
superimposed structures (delete overlapping bases and so on). Care is
needed in deciding what to keep/remove depending on the features of your
structure. If your structure is a protein-bound DNA it may be deformed
and then you'd like to keep as much as possible from the original
structure. Same is valid if your structure has a particular conformation
you are interested in .... We usually do a minimization/equilibration in
which the extensions are allowed to move while the structure not (not
sure this is really needed always)

Now, if your DNA is B-DNA, this procedure works quite easily . However,
if you have a special DNA structure, you need to get some experience
with NAB to build exactly the type of structure you need. Especially the
overlapping parts between extensions and structure you probably want to
have them in a conformation that is the same as in the structure


On 19/01/2021 04:57, Airy Sanjeev wrote:
> I have a protein that is bound to DNA, now I need to extend the DNA
> structure at both ends. Kindly guide me how to extend the DNA using any
> software.

Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Tue Jan 19 2021 - 02:00:02 PST
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