VMD-L Mailing List
From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Oct 05 2004 - 11:44:53 CDT
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Hi Meric
If I am not mistaken, you can't calculate the phi angle for the first
residue of the protein, because you are lacking the previous carbon atom.
The same thinking applies to the c terminus.
Regards
Brian
On Sat, 2 Oct 2004, Meric Ayse Ovacik wrote:
> Hi all;
> I need phi angle for the first residue in a chain, and psi angle for the last residue.
> VMD gives them as zero. Is there a way to calculate that angles?
> I do have the script for the dihedral angle calculation. However, I cannot decide which atoms to use
> in order to calculate phi angle for the first residue in a chain, and psi angle ror the last residue.
> thanks in advance...
> Ayse Meric Ovacik
> Koc Universitesi
> 02123381736
> http://home.ku.edu.tr/~movacik
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**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
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