How to generate a Methylated DNA pdb file from sequence to be use in MD

[bciezah1]

Hello everyone,

I am new in this about MD using nucleic acid and I wonder, maybe this is a silly question, if there is a way to generate a pdb file from my dna sequence where some nucleotides are methylated, also I wonder if there are force field and parameter field available for them.

Thank you very much in advance,
Basilio.

[xiangjun]

It is a vague question (to me). There may be standard protocols for handing methylation or other types of DNA/RNA modifications in the MD field. I'm not a practitioner of MD simulations, and do not know "if there are force field and parameter field available for them".

As far as 3DNA is concerned, you could try "fiber" and then "mutate_bases" (plus other 3DNA utilities) to get the started. See the FAQ entry "How can I mutate cytosine to 5-methylcytosine" for the most common case.

HTH,

Xiang-Jun

[bciezah1]

Dear Xiang-Jun,

Thank you for your soon answer. Sorry if my question was not clear. I was wondering if 3DNA has the option you just mentioned. I could see it does. I will review it right away.

Best wishes,

Basilio.