Hi AMBER community,
I wanna ask about your expert advice on using the available DNA force field
in modeling and simulating a hairpin ssDNA. I am planning to use OL15
and/or PARMBSC1 for the DNA.
Question 1: I will be simulating a protein-hairpin DNA interaction. I am
not interested in the hairpin - linear DNA transition, I just need to study
extensively how the DNA will interact with the protein. Just wanted to
confirm that OL15 or PARMBSC1 will work fine with ff19SB and TIP3P protein
and water force fields for this purpose.
Question 2: The other question I have is how do you parameterize a modified
DNA where instead of having a cytosine in one of the nucleic acid, I will
modify it to other nucleotide-like unit (see Figure 1 of
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00803-6 ) .
Can I still use OL15 or PARMBSC1 force field for that?
The other conflict is that I cannot use GAFF or GAFF2 since the whole thing
would be more than 200 atoms total.
Question 3: What tool do you use to modify the DNA structures and which DNA
library in tleap do you use for such modifications like the one in Figure 1
of the above references ? Should I still antechamber this even though it is
super huge for antechamber?
Thank you for your insights!
Sincerely,
Kevin
Mac Kevin Braza
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Received on Wed Feb 28 2024 - 17:00:02 PST
