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I need a code/app/website that can receive a DNA sequence, for instance AATCT, and output a file with the atomic coordinates.

I used to do this on this website but the service is no longer working and I haven't mange to find a substitute.

I found a code that does this but doesn't include de H atoms .

I have also visited some data banks but they don't have what I'm looking for, I want to have control over the DNA sequence I want.

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If you know the program AMBER, There is an option where you write an input with the sequence that you want, automatically the program will build the two strands, and your output will be pdb format. Or You can use Avogadro program direct and you will write the sequence and the output will be XYZ format.

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The output

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For batch use, I recommend Open Babel which can translate fasta format DNA sequences into single or double-stranded DNA coordinates. (Indeed, it's used in Avogadro.)

FASTA format:

> DNA
AATCT

Then you can use something like this (documentation)

obabel file.fasta -O file.pdb # output double-stranded
obabel file.fasta -O file.pdb -a1 # output single-stranded

And of course file.pdb could be file.sdf or file.mol2 for other formats supported by Open Babel.

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