On Tue, Jul 18, 2023, Sneha Kandapal via AMBER wrote:
>
>I am creating a topology file for methylated DNA and encountered the below
>error. I will appreciate if somebody can explain what does .R<DC5 1>.A<P
>29> mean in the attached pdb file.
By default, Amber assumes that the 5' nucleotide does not have a phosphate
group. You would need to load the "terminal_monophosphate.lib" file before
your loadPDB line, in order to get 5' nucleotides with a phosphate group
attached.
....dac
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Received on Tue Jul 18 2023 - 10:30:02 PDT
