Nucleic Acids (DNA, RNA)

DNA and RNA molecules can be generated directly from primary nucleotide sequence data. This can be input directly, or inferred from an opened protein based on its amino acid residues. In the case of the latter, we make arbitrary choices when multiple nucleotide triplets correspond to a given amino acid.

DNA can be generated as either single-stranded, or double-stranded molecules.

Molecular Dynamics

You can perform molecular dynamics on nucleic acids acids without any special setup. We use Amber's OL3 force field parameters for DNA, and RNA parameters for RNA.