Hello!
You can use the AMBER parameters (prep and frcmod) available in:
http://amber.manchester.ac.uk/
for deoxy-5-methylcytosine (dmc).
Hope that helps!
Rodrigo.
On Thu, Jul 13, 2023 at 12:22 PM Sneha Kandapal via AMBER
<amber.ambermd.org> wrote:
>
> 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 - 12:00:02 PDT
