[gmx-users] g_angle output

UCT Staff Member - Jackson Jackson at SCIENCE.uct.ac.za
Fri May 20 12:41:54 CEST 2005

I have a cyclic peptide which when I start a high temperature dynamic
run has all peptide bonds trans.  After cluster analysis of the
trajectors I find the lowest energy conformation to have two cis peptide
bonds.  I am now trying to monitor the peptide dihedral angles during
the run to see when  this trans/cis isomerisation occurs. 
I have used:

g_angle -f xx.trr -s xx.tpr -n xx.ndx -all

I am then prompted to select an angle from the index list. I have to
repeat this for every angle in the list.
I have 2 questions:
How do I get g_angle to do the whole list automatically?
What does the output mean?  Accoding to the manual it should have the
average and the individual angles.  However if I look at the file for
one of the angles it has 3 columns, the time and 2 angles.  The first
angle does not look like the average.

Professor Graham E. Jackson
Department of Chemistry
University of Cape Town

Tel: (021) 6502531
Fax: (021) 6897499

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