Dear All, I am interested in charting the trajectory of the ligand with respect to the residues of the binding pocket, during the simulation. May be representing the center of mass of the ligand as a dot at each frame, would help us see the path traced by the ligand in the pocket, during the simulation. Is there a possibility to do this during the trajectory analysis period / post production..? I was wondering if we could perform PCA and impose the ligand's trajectory on the bound complex and visualize only the ligand's movement with respect to the amino acid residues of the binding pocket. But this would not give a clear idea as the residues in binding pocket also move during the course of simulation. Hoping that i was able to explain it well enough.. Thank you in advance.
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