I am simulating a system with an amyloid protein and a phenylene ethynylene oligomer. I would like to look at the planarization of the ring groups of the ligand over time but the dihedrals are separated by multiple atoms. Would it be valid to choose a dihedral that isn't four atoms in a row to determine the restriction of rotation when bound to the protein surface?
Thank you for your help.
Tye Martin
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Received on Mon Feb 11 2019 - 13:00:03 PST
