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@@ -72,6 +72,8 @@ The `LAMMPS_oxDNA.py` script takes one mandatory argument and outputs two files.
* An oxDNA topology file (named by suffixing the LAMMPS output file with ".top")
* An oxDNA configuration file (named by suffixing the LAMMPS output file with ".oxdna")
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## oxDNA-to-PDB converter
The `oxDNA_PDB.py` script takes three mandatory arguments and outputs a single file. Since oxDNA bases has no one-to-one explicit mapping to all-atom representations, the converted structure will most likely require some sort of relaxation procedure before being used as input for all-atom simulation packages. Moreover, when using this script the following points should be taken into account: