Hi, I have simulated (3ns) the crystal str of GFP (pdb -1GFL, without chromophore formation) and a modeled variant of GFP with a change in loop region (loop length is extended) . After calculating the RMSD of both strs. and superimposing reveals that RMSD doesnot fluctuate much for the modeled str (though it doesnot exactly superimpose on the RMSD of the crystal str of GFP) . I want to carry out Essential dynamics of both the structure and want to locate which region shows minimal and maximal amplitudes of motion (ie. whats the cause of this fluctuation) ... i need help in this regard ??
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