On Wed, Sep 20, 2023, Claire Harmange Magnani via AMBER wrote:
>
>Other than attempting to download an older version of Ambertools, what
>other options do I have to build and modify DNA structures so that they
>will be compatible with Amber?
"Compatibility with Amber" is the least of your problems. Any software that
can create a PDB-format set of coordinates should work. It helps if that
software uses IUPAC/PDB nomenclature, since that is what Amber uses. But
it's usually pretty trivial to convert some set of atom names to the
standard.
>I had hoped to familiarize myself with Amber by following this tutorial
><https://ambermd.org/tutorials/basic/tutorial1/>
That tutorial is fine, but note that (as with all MD runs) one needs a
starting conformation. NAB is one way to generate those, but plenty of
other pieces of software can also do this. (A *lot* depends on what sort of
DNA structures you have in mind, so it's hard to be more specific.)
><https://bionano.physics.illinois.edu/sites/default/files/x3dnatutorial_0.pdf>.
Note that this seems to be exclusively aimed at double-stranded DNA (perhaps
with modified nucleotides.) Creating model of double-stranded DNA is pretty
easy, even in Amber. Althought the NAB program for this (used in the old
tutorial) is no longer present, the fd_helix program is still there, in
nabc. So if you interest is in double-stranded DNA, just play around a bit.
....dac
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Received on Wed Sep 20 2023 - 20:00:02 PDT
