How use GROMACS for circular DNA simulation?

25 September 2022 0 2K Report

I would like to ask about the simulation about circular ssDNA in GROMACS. Because running the pdb of circular ssDNA through pdb2gmx will lead to terminal related errors, I have conceived a solution to fix this problem, separating PO2 from the phosphate group PO4 connected between 5 'and 3' of the circular DNA as a new residue, and writing dna.tdb and specbond.dat, to link the two terminal oxygen atoms with the phosphorus atom of PO2. Is this method feasible? My thoughts are as follows

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