Dear All,
I have a protein structure with 82.9% Ramachandran favoured (high percentage of Ramachandran allowable and outlier). With tough equilibration, I have run a 30 ns production MD of that protein. But I find the PDB at 30 ns is still only with 83.84% Ramachandran favoured (still high percentage of Ramachandran allowable and outlier).
Will you please explain why the MD process did not lead to the ideal protein state, i.e., with more than 99% Ramachandran favoured?
Best regards.
Brett
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Received on Sun Sep 20 2015 - 05:00:04 PDT
