Hi, I was trying to run MD simulation of my protein in DMSO. I used the force field ffG53a6 and did the energy minimization after solvating the protein in DMSO box. But after solvating in DMSO, the structure is changing. My protein is a homodimer and the loop at the dimer interface is converting into a sheet. Please suggest where I am going wrong since the structure shouldnot change after solvation.
Regards Swagata Chakraborty Research Scholar, Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai-400005
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