[gmx-users] dihedral parameters in oplsaa

[friendli]

Hi gmx users,

In order to understand the oplsaa all atom force field, I use pdb2gmx to 
generate topology file of a pdb which contains only one AA( the glycine).

After the EM simulation, I use gmxdump to look for the details of the 
parameters.

I find,
in .top file, there are 15 proper dihedrals under directive [dihedrals] 
and the funtion type is 3 (i.e. RB dihedrals).
However, in the output generated by gmxdump, there are explicit 
parameters for only 9 of these dihedrals.  The 9 dihedrals corresponds 
to 9 of the 15 in .top correctly, but the other 6 are missing.

In the six missed dihedrals,  two are for N-CA-C-O, four are for  HA-CA-C-O.

Can anybody give a hint on this? Is there any default value not output 
by gmxdump? All other parameters are fully printed.


     H   H  O
      |    |    | 
H- N - C - C = O
      |
     H

thank you

LQ