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

PeiQuan Chen gromacs at 163.com
Fri Oct 10 14:38:01 CEST 2003

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
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
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	

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