[gmx-users] query regarding mk_angndx

[Kavyashree M]

---------- Forwarded message ----------
From: Kavyashree M <hmkvsri at gmail.com>
Date: Fri, Mar 8, 2013 at 10:45 PM
Subject: query regarding mk_angndx
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


Dear users,

I used mkang_ndx to create an index file with dihedral angles.
Input was:
mk_angndx  -s  a.tpr  -n  angle.ndx   -type   dihedral
output angle.ndx read like this -
[ Phi=180.0_2_43.93 ]
     5    20    18    19    22    37    35    36    27    32    30    31
    39    59    57    58    61    76    74    75    66    71    69    70
...

According to my understanding the numbers indicate the 4 atoms
defining the particular dihedral angle.
But when I checked the pdb file for these atoms-
ATOM      5  CA  MET A   1     111.430  40.170 113.130  1.00  0.00
ATOM     18  C   MET A   1     112.060  41.020 112.030  1.00  0.00
ATOM     19  O   MET A   1     111.910  42.240 112.010  1.00  0.00
ATOM     20  N   GLN A   2     112.940  40.430 111.220  1.00  0.00

I could not make out how this defines phi?
Kindly clarify my confusion.

Thank you
kavya