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I need to generate a pdb for ssDNA to research the interaction of DNA and proteins. I will really appreciate if you can please guide me. Thank you all for your time.

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A related question on SeqAnswers does not seem to have meaningful current answers.

However, a question on ResearchGate points helpfully to this RNA structural modeling server (RNAComposer) that might be useful, once you create secondary structure predictions. Secondary structure is not enough to predict information needed for a PDB.

An alternative somewhat older path to a PDB for RNAs would seem to be MC-fold and MC-sym.

Granted: most of this is for RNAs, which will have a somewhat different structure and mode of folding.

The toolkit seems a little less rich for DNA, but you can still use tools such as ViennaRNA for secondary structure prediction, and there do seem to be some recently published tools for DNA structure prediction (see also here).

There are some further DNA/RNA resources here that may be helpful.

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