Hi, I did a 3ns simulation of a 236 amino acid protein (GFP, a beta barrel protein), after checking the trajectory it seems that from the first frame itself almost half portion of the two beta strands (159-171, 174-187) of GFP got converted into a loop like structure .. which should not happen in general.. and this change is found to be present from the first frame itself... So I want to know where can the fault be ... I followed the instructions for simulation from the lysozyme tutorial.. Pls help ..
-- Bharat Ph.D. Candidate
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