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I have two .pdb files with two ssDNAs, which should form some specific shape when closed together. Is it possible to model/simulate this merging somehow?

I would preferably like to have a program that would take both .pdb files as input and return .pdb file of the combined molecule.

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If the structures are relatively small (< 4 nt), you can use Chem3D (from PerkinElmer ChemOffice software): Load both of the PDB files and run an MM2 minimization task. For more complex structures GROMACS or similar molecular dynamics tools are used.

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