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I have a PDB structure for DNA minicircle. To run the simulation, I have to create the topology file, which I am doing using Tleap. But Tleap automatically converts my terminal bases (in the PDB...
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Why a canonical AMBER simulation of DNA doesn't include dangling 5' phosphate? So, if I want to simulate an oligomer of length N bp, then it will have 2N bases but 2(N-1) phosphate when standard...
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