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

[bharat gupta]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110126/27d1cb66/attachment.html>