I'm trying to replicate a protocol from "Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors" and I'm having some problems with the 3rd step which includes the change from RNA to DNA, the protocol explain that I have to change te ribose sugar with doaxyribose using the AutoPSF plugin and that I have to manualy change the uracil but it seems that this plugin doesn't allow me to do those changes. I want to know if someone who knows how to use VMD can explain me how to do these steps without failling.
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