Minimization question
In a two domain protein, I randomize the phi and psi angles of the interdomain linker and then energy minimize, considering only repulsive VDW. Oddly, about one third of the time, the minimization step increases the energy. Possibly the minimization function is considering only the residues that are allowed to move, but that that score function is considering the entire system. If this is what is going on, it is not what I expect or want, I'd like the minimization function to consider the entire system. Below is the python script.
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