I have a DNA molecule and a chemical compound. The compound is experimentally known to cause alkylation and base modifications. I want to show the interaction of DNA and the compound in silico and also want to see the effect under different conditions of temperature, pH etc. How do I go about it?
I am not an expert on computational chemistry and have only played a bit with molecular dynamics of oligonucleotides, and what you want to do would require a docking and then a complex QM/MM approach with molecular dynamics.
In my experience, to get useful information from computational methods you need to ask specific questions. Expecting to find explanations of general variables is not realistic with this system you describe.
By the way, it would be nice to have some X-ray or NMR as starting point, otherwise you are off solid ground right from the beginning!
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