[gmx-users] improper_Z_N_X_Y & improper_O_C_X_Y

[Erik Lindahl]

Nguyen Hoang Phuong wrote:
> Dear All,
> 
> What is the meaning of the "improper_Z_N_X_Y" and "improper_O_C_X_Y" in
> the file ffoplsaa.rtp? Should I change them when I build the new
> molecules? Gromacs creates the dihedral angles automatically?
> 
> Thanks for any explaination!
> 

Yes, dihedrals are created automatically, but not improper dihedrals.

The improper dihedrals for OPLS are defined in ffoplsaabon.itp, but 
since it is an all-atom force field you only have to use it for planar 
groups (e.g. uncharged -NH2) and not chiral atoms like aminoacid 
alphacarbons.

If you need to add an improper dihedral you should look up the four-atom 
definition in the manual, and then determine which one in 
ffoplsaabon.itp fits best. (X,Y,Z denote any atom).


Cheers,

Erik