Hello,
This question is about methylated DNA. I am working with ds(DNA) of 12 base pairs ds(CGCGCGCGATCG). By using Avogadro software I changed the third base (cytosine) to methyl cytosine and generated a pdb file.
My question is I followed the tutorial in AMBER for simulating DNA. However, I am not sure whether I need to follow exactly the same steps for methylated DNA. As I read in some old threads that we need to calculate the RESP charges.
I will appreciate if you could please guide with the protocol or any other way I can change specific cytosine to methylated cytosine and perform MD simulation.
Thank you.
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Received on Thu Jul 13 2023 - 11:30:02 PDT
