AMBER Archive (2007)

Subject: AMBER: native contact analysis!

From: r. a. (rosajaan_at_yahoo.com)
Date: Wed Feb 21 2007 - 20:52:37 CST

Dear amber users
   
  Hi...
  I m studying thermal unfolding using MD. at first step, I ran a 1ns simulation for 300 K as a control. now i need to prepare a native contact map for the protein. To be defined as a native contact, the 2 nonsequential c-alpha atoms of the reference structure have to be within 6 Angstrom of each other and the average occupancy of this contact must be >70% over the course of our control simulation at 300 K. i referred to papers but I couldnt find much about how they did such a calculation through their methods and materials. I would like to know that we can do it using e.g. ptraj, if so how. any suggestion or comment about using other softwares?...thank you all in advance...
   
  Regards
   

 
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