In Abalone (http://www.biomolecular-modeling.com/Abalone/index.html) you can create your own templates both residues and conformational templates. See, for example, on the internal B-DNA and peptides templates.

Dear Amir,

Nucleic acid builder (nab) is a high-level language that facilitates manipulations of macromolecules and their fragments. nab uses a C-like syntax for variables, expressions and control structures (if, for, while) and has extensions for operating on molecules (new types and a large number of builtins for providing the necessary operations).I expect nab to be useful in model building and coordinate manipulation of proteins and nucleic acids, ranging in size from fairly small systems to the largest systems for which an atomic level of description makes good computational sense. As a programming language, it is not a solution or program in itself, but rather provides an environment that eases many of the bookkeeping tasks involved in writing programs that manipulate three-dimensional structural models.

There is a web server http://haddock.science.uu.nl/dna/dna.php which allows you to do so...however you need a template for building the structure or atleast you should be aware of the step parameters(which can be used as an input in this server)