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
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