Re: [AMBER] Query regarding DNA

From: Matias Machado <>
Date: Fri, 11 Oct 2019 18:10:47 -0300 (UYT)

Just a follow up comment to David's...

The mechanical properties of single and double DNA molecules are very different, in particular the persistence length of the former is about a few base pairs while the later is about a hundred... just watch this nice talk from Thomas Cheatham [] or look at this paper [].

So I see no sense in generating a double stranded DNA from a single one, the conformations simply won't match (see e.g. PDB 1EW1 or 2KH4)...

Hence, I suggest you to build the double stranded DNA from scratch by using the NAB utility in AMBER Tools.

Still, I'm wandering if your question was motivated by downloading a PDB structure of a double stranded DNA from the PDB but seen only one strand (e.g. PDB: 4OCB), in which case you must download the biological assembly... Notice, to see both chains at the same time in VMD, you have to remove the ENDMDL statement.



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "David A Case" <>
Para: "AMBER Mailing List" <>
Enviados: Viernes, 11 de Octubre 2019 14:31:52
Asunto: Re: [AMBER] Query regarding DNA

On Fri, Oct 11, 2019, Saikat Pal wrote:

>Dear all,I have a PDB that contains only one strand of DNA.  How to add
>the complementary strand?

Depends a lot on where the PDB file came from, and what the conformation
of the single strand is. I don't think it's worth trying to describe
all the various possibilities here -- can you just tell us more about
your problem?


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