Dear All I am trying to refine a protein model which is a homodimer with each chain having 609 residues.I tried minimizing in Chimera and then checking models with procheck.Infact model quality deteriorated as far as Ramachandran plot is concerned. Will doing MD simulation help me in Gromacs. It is a big protein so long MD simulation is not possible. Short duration MD will be insufficient to search native structure. I am stuck-up. Can anyone on this list help me. Shahid Nayeem
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