Hello!
I wrote an example on how to use the PREP and FRCMOD to include the
methylated cytosine in a duplex DNA and generate the topology and
coordinates. Let me know of any questions or errors you find!
https://amberhub.chpc.utah.edu/simulation-of-a-10-mer-dna-with-a-deoxy-5-methylcytosine-residue/
Hope that helps!
Rodrigo.
On Thu, Jul 13, 2023 at 12:10 PM Sneha Kandapal <Sneha.Kandapal.uga.edu> wrote:
>
> Thank you for your reply. But I did not understand how to use those parameters. I am new to this AMBER and am following this tutorial Simulating a DNA polyA-polyT Decamer (ambermd.org). I have no idea where I can use those parameters.
>
> I will appreciate if you could please provide some links/tutorials that might help in understanding.
>
>
>
>
>
> From: Rodrigo Galindo-Murillo via AMBER
> Sent: Thursday, July 13, 2023 2:46 PM
> To: Sneha Kandapal; AMBER Mailing List
> Subject: Re: [AMBER] Methylated DNA simulation
>
>
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
>
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jul 13 2023 - 23:30:02 PDT
