[gmx-users] Re: change in the secondary structure after simulation

bharat gupta bharat.85.monu at gmail.com
Thu Jan 27 06:11:22 CET 2011


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 ..

Ph.D. Candidate
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