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7.2 years ago
I have a homology model of a protein. I have to do energy minimization for the same, I have chosen to do this using Avogadro software. My doubt is, should I start "Optimize Geometry under Select menu" or "Auto Optimize tool"? I chose Avogadro because, when I did the same using GROMACS, the protein chains got split and looks totally disrupted. When I tried using ArgusLab to optimize Geometry, I ran like almost 30 steps, still the Geometry did not converge.
