[gmx-users] A strange phenomenon in the new version opls-aa force field

[PeiQuan Chen]

Dear gmx-users:
  
>The main reason why I only uploaded it to the contrib section is that
>I have changed my development version of pdb2gmx not to remove any
>dihedrals over bonds with impropers (which pdb2gmx used to do
>automatically), but I haven't tested it with the "vanilla" version of
>pdb2gmx.
The old version *.rtp file:
 [ impropers ]
     N    -C    CA     H    improper_Z_N_X_Y 
     C    CA    +N     O    improper_O_C_X_Y
The new version *.rtp file:
 [ impropers ]
    -C    CA     N     H    improper_Z_N_X_Y
    CA    +N     C     O    improper_O_C_X_Y
  
      O
      |
   CA-C-N
I noted that you have changed the cetral atoms(N or C) from the position 1 to the position 3.
I think the atom order of the old version is correct. Becuase in the opls-aa force field, we use
proper dihedrals [1+cos(2*x+180)] to model improper dihedrals. The improper torsion angle should be 
defined as the angle between planes(C, CA, +N) and (CA,+N,O). But inn the new version *.rtp file, the 
impropers section define the angle between planes(CA,+N,C) and (+N,C,O).

Why you changed the atom order for improper torsion? Could you give me detail explanation?


Sincerely yours
---- 
PeiQuan Chen
________________________________________________________________________
PeiQuan Chen 	Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223506728		Mobile Phone: (+86)13920675030
gromacs at 163.com	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++