Here we provide a set of input files for the various conversion modules.
- XYZ → oxDNA: download a centerline file that can be converted into an oxDNA configuration of a ring made of 210 bases.
- cadnano → oxDNA: download a cadnano json file that can be converted into an oxDNA configuration of a small tile-like structure made of 3 strands (128 nucleotides in total).
- LAMMPS → oxDNA: download a LAMMPS data file containing the coordinates for a duplex made of 8 nucleotides.
- PDB → oxDNA: download a PDB file containing the all-atom coordinates of a Dickerson dodecamer.
- Tiamat → oxDNA: download a Tiamat json file that can be converted to an oxDNA configuration of a duplex made of 13 nucleotides.
- CanDo → oxDNA: download a CanDo file that can be converted to an oxDNA configuration of a four-way junction made of 64 nucleotides.
- vHelix → oxDNA: download a vHelix file that can be converted to an oxDNA configuration of a wireframe origami made of 1488 nucleotides.
- oxDNA → LAMMPS and oxDNA → PDB: download a zip file containing an oxDNA configuration (ds.dat) and topology (ds.top) of a duplex made of 8 nucleotides. The pair of files can be used as a starting point to obtain a LAMMPS data file or a PDB all-atom configuration.
Configurations generated from XYZ, cadnano, Tiamat, CanDo, vHelix and PDB files will almost invariably require some equilibration. For the case of the XYZ, Tiamat, CanDo, vHelix and PDB to oxDNA modules, it is common to find locally-stressed portions of the DNA structures which contain steric clashes, are over-bent/twisted or in which distances between the backbone sites are too large. All these local stresses could lead to numerical instabilities in an MD simulation. With oxDNA, a standard relaxation procedure starts with running short (103 to 104 steps) Monte Carlo simulations on a CPU, followed by order of 106 steps of an MD relaxation with a maximum-value of the cutoff for the backbone potential (ideally on CUDA, as simulations of large structures are prohibitively slow on CPU). Sample scripts for the MC and MD relaxations can be downloaded here and here, respectively. More documentation and examples can be found in the oxDNA package or in its webpage.
Regarding the cadnano → oxDNA module, the conversion procedure leads to a three-dimensional structure that will almost inevitably require a relaxation procedure with significant human interaction. The main reason is that cadnano does not consider structural constraints apart from crossover positions, and the three-dimensional structure of the converted file might differ significantly from the final and intended design.. The most obvious problem to solve during the relaxation pertains to the presence of strands with some backbone bonds that are unphysically overstreteched. These can in principle be relaxed automatically, but it is important that the quasi-topological features of the resulting structure are monitored: during relaxation, overstretched backbone bonds may cross each other in some wrong way. In our experience, this problem is not very common but it is a possible reason for unsuccessful relaxation. When it does happen, a possible way to overcome quasi-topological problems is to relax bonds in some system-specific order.
The internal structure of double and single stranded sections will also differ from the typical configurations that these adopt in a relaxed origami. The base pairs that have to be present by design in the double-stranded sections do not usually have a very low energy, and the stacking between consecutive bases is not completely optimal. This is because a regular structure with the required periodicity is not the energy, nor the free-energy, minimum for the oxDNA potential. The required structural changes are local for this kind of issues, and therefore usually happen very quickly and can be resolved by energy minimization.