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 file) into 5' and 3' blunt ends. So, basically, it creates a topology file for a DNA minicircle with discontinuity in the backbone i.e. treats it like a double-stranded linear structure.

Here is the Tleap input I am using,

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source leaprc.water.tip3p

source leaprc.DNA.bsc1

dna = loadpdb "INDEX.ends.nab.pdb"

solvateOct dna TIP3PBOX 10

addIons dna Cl- 0

addIons dna K+ 0

addIons dna Cl- 206

addIons dna K+ 206

savepdb dna INDEX.prerand.pdb

saveamberparm dna INDEX.prerand.top INDEX.prerand.crd

quit

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Any lead in this direction will be a great help. If possible, please share some scripts.