[gmx-users] improper dihedral and proper dihedral

[Dongsheng Zhang]

Dear David,

Thank you very much for your reply. After I study ffoplsaa.rtp and
discuss with my colleague, I have better understanding with improper
dihedrals. However, I still have some questions:

1. If four atoms form an improper dihedral, only when the central atom
is N or C (with double bonds), we will assign that improper dihedral in
Gromacs. Is it correct? Could you please tell me how to make the
sequence of those four atoms (The third one is the central, how about
others?)? I think the sequence is important because we will use the
outer two atoms to define the improper dihedral parameters (angle and
constant) in *.itp (e.g. ffgmx2bon.itp).

2. When I check ARGN in the file ffoplsaa.rtp, I found five impropers:


 [ impropers ]
    -C    CA     N     H    improper_Z_N_X_Y 
    CA    +N     C     O    improper_O_C_X_Y 
    CD    CZ    NE    HE    improper_Z_N_X_Y 
    NE   NH1    NZ   NH2    improper_O_C_X_Y 
    CZ  HH21   NH2  HH22    improper_Z_N_X_Y 

 I think there is a typo in the third improper dihedral, the third atom
should be CZ, not NZ.

3. It surprises me that there is no (proper) dihedral for ARGN in the
file ffoplsaa.rtp. For most amino acids, there are two common dihedrals:

  N    CA    CB    CG     dih_***_chi1_N_C_C_C
 CG    CB    CA     C     dih_***_chi1_C_C_C_CO

why does Gromacs not assign any dihedral to ARGN?

Could you please tell me how to decide which dihedrals we need to assign
to Gromacs? 



Have a nice day!

-- 
Dongsheng Zhang <dong at pampas.chem.purdue.edu>