On Mon, Nov 25, 2024, James Kress via AMBER wrote:
>Is there any tutorial or descriptive process I can use to build a DNA
>oligomer with a 5-methylcytosine modification that will work in AMBER? I've
>searched the AMBER website, the list archives and the web but cannot find a
>descriptive process for building this entity.
All kinds of modified DNA and RNA nucleotides (including 5-methylcytosine)
are covered in the recently released libXNA project:
https://doi.org/10.1021/acs.jctc.4c01164
There happens to be a 5-methylcyotosine specific tutorial(!):
https://modxna.chpc.utah.edu/duplex-with-methylated-cytosine/
..good luck...dac
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Received on Tue Nov 26 2024 - 09:00:03 PST
