Introduction
The following script takes a given DNA base sequence and builds a coarse grain DNA model with it. For example an input of "ATCGGCATC" would generate a model of 9 base pairs following the given sequence. As soon as the calculations are complete, the user will be prompted to download the generated PSF, PDB, and a CRD file for the coarse grain model and a PDB of the all-atom model. The download page will be displayed after calculations and processing takes place (up to 2 minutes), and will contain energies for verification.
Download Source Code
Linux Source Code with Makefile (tar.gz)
Windows Source Code with Executable (zip)
Coarse Grain DNA Model Builder
* The 2009 version is a re-parameterization of the 2007 version. Both use the same geometries. The 2007 version is most appropriate for studies of duplexed DNA (viral packaging, histone wrapping, etc.). The 2009 version is most appropriate for studies involving DNA hybridization.
** In the 2009 version, the dielectric constant is temperature dependent. In the 2007 version, the dielectric constant is constant at 78.
Citing
If you use this generator in your work, please cite the appropriate sources:
T. A. Knotts, N. Rathore, D. C. Schwartz, J. J. de Pablo. A Coarse Grain Model for DNA. J. Chem. Phys. 126, 084901 (2007).
E. J. Sambriski, V. Ortiz, J. J. de Pablo. Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways. J. Phys.: Condens. Matter 21, 034105 (2009).