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 [
https://www.youtube.com/watch?v=JBYfQ9mUFo8] or look at this paper [
https://doi.org/10.1016/j.bbagen.2014.09.007].
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.
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "David A Case" <david.case.rutgers.edu>
Para: "AMBER Mailing List" <amber.ambermd.org>
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?
...thx...dac
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Received on Fri Oct 11 2019 - 14:30:02 PDT
