[gmx-users] atom names in ffbonded.itp (oplsaa.ff)

[Mark Abraham]

On 19/10/2011 3:50 PM, mu xiaojia wrote:
> Dear gmx-users,
>
> Does anyone know where can I find any explanations about the atom 
> names in ffbonded.itp file in oplsaa.ff? I am trying to compare the 
> amino acids' parameters in gromacs 4.5.4 with in tinker. Or where to 
> find the default parameters gromacs takes for amino acids in its 
> aminoacids.rtp file?
>
> For example, it is hard to guess what are C*, C_2  and C= in 
> ffbonded.itp file:
>
>  C*    HC      1    0.10800   284512.0   ;
>   C     C3      1    0.15220   265265.6   ; END
>   C_2   C3      1    0.15220   265265.6   ; END
> ...
> C=     C=     HC      1   120.000    292.880   ; wlj
>   C      C=     HC      1   119.700    292.880   ;
>
> Thanks!
>

You need to cross-reference the OPLS atom types (full description in 
their literature, partial description in atomtypes.atp) with the atom 
names in ffnonbonded.itp to make ffbonded.itp more clear.

Mark