AMBER Archive (2006)

Subject: AMBER: dihedral angle problem

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Fri Dec 08 2006 - 16:53:32 CST

Dear Amber users,
   
  I have a problem to calculate the dihedral angles. Since there are 2 amino acid in the 2 sides of the main chain, I want to use hte diheral angle to discibe it. But after I calculate the the dihedral angle through "dihedral" command by specify 4 atoms for each of amino acid, I found theri angles are similar. How can I define the dihedral angle direction in the calculation? Or maybe there are some other ways to do it. Any suggestion will be greatly appreciated!
   
  Bests

Esther B.

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