Off-lattice CanDo online submissions using Tiamat and CNDO file formats are no longer available. Off-lattice CanDo can be run locally using the source code available here: Off-Lattice CanDo. In order to run off-lattice CanDo locally, external program requirements are MATLAB, ADINA, and UCSF Chimera.
The source code for off-lattice CanDo is available here: Off-Lattice CanDo. To run off-lattice CanDo locally, external program requirements are MATLAB, ADINA FE Solver, and UCSF Chimera.
The above submission link is suitable for simulating DNA assemblies in which DNA duplexes are placed freely in 3D space. The link accepts design files that are first prepared with the software Tiamat  and then parsed by running the parser locally. The link performs analysis using a finite-element-based modeling framework for DNA with single base-pair resolution. The procedure is demonstrated in the tutorial.
Users of this submission link are kindly requested to cite the following two references:
- K Pan, DN Kim, F Zhang, MR Adendorff, H Yan, M Bathe. Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nat. Commun., 5, 5578 (2014).
[ PubMed Article ]