I have been programming a tool for protein structure analysis and I was looking for any method or software where I can rapidly introduce perturbations on a given molecular structure (PDB format). Like Rotameric Induced Perturbations, but the main requirement is to use primarily free or open software. I thought of steered molecular dynamics protocols, but they are not fast enough for me to process tons of PDB structures.
In other words, I just want a software that would move some atoms on ta structure in a way that wouldnt cause clashes and "impossible" structural states.
Thanks in advance.