AMBER Archive (2006)

Subject: Re: AMBER: dihedral angle problem

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Fri Dec 08 2006 - 19:00:48 CST

Thanks for your reply and helping me clearify my question.
  I question is how to correct to calculate the dihedral angle of E-F-a-b and a-b-C-D. Since E-F and C-D in the deffrent side of a-b, is it possible to describe it by the negative and positive dihedral angle?
   
  E-F
      -a-b
          -C-D
   
  Thank you very much!
   
  
"David A. Case" <case_at_scripps.edu> wrote:
  On Fri, Dec 08, 2006, Esther Brugger wrote:
>
> 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!

I think you will have to be clearer, maybe by giving an example or more
information. When you say "dihedral angle direction", it's not clear whether
you mean to distinguish between positive and negative dihdral angles, or
to think about the (unimportant) distinction between a-b-c-d and d-c-b-a,
or whether you mean something else altogether.

Also, the phrase "there are 2 amino acids in the 2 sides of the main chain" is
hard to understand. I'm not tyring to criticize, just to get enough specific
information to allow someone (else?) to answer the question.

...dac

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Esther B.

 
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