[gmx-users] Parametrisation of the heteroatomic pdb

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 10 17:14:38 CET 2011

On 11/11/2011 3:01 AM, James Starlight wrote:
> Mark,
> I've mistaken
> I need to invert impropers for DIHEDRAL for Calpha atom. By this way I 
> want to change L form to D form for Gromos ff. Does this correct ?
>  [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>   -CA    -C     N    CA     gd_14
>    -C     N    CA     C     gd_39
>     N    CA    CB    CG     gd_34
>     N    CA     C    +N     gd_40
>    CA    CB    CG   CD1     gd_34

I've no idea what any of the above was intended to mean. I'll repeat 
myself again, there's nothing about the improper dihedrals that enforces 
a particular chirality. Proper dihedrals also don't care about 
chirality. Chirality is set in the starting configuration, and merely 
preserved by the force field.

> So I think that I need to make corrections in that gd_n  files. But in 
> what exactly and where in manual could I read about that parametrisation ?

See the #defines in ffbonded.itp. The implementation of the GROMOS force 
fields are a bit idiosyncratic this way.


> It could be cool that in that section such information present :)
> http://www.gromacs.org/Documentation/Terminology/Dihedral?highlight=dihedral
> 2011/11/10 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>     First, identify that there's anything to invert. Look at the
>     #define lines for gi_1 and gi_2 and the manual sections for
>     impropers. There's nothing associated with any handedness. The
>     impropers for chirality prevent inversion, rather than enforcing a
>     particular chirality. You can test this yourself. Make a .tpr of
>     an L-amino acid and .gro files of each chirality, and then use
>     mdrun -rerun Lconfiguration.gro -s Lconfiguration and compare with
>     mdrun -rerun Rconfiguration.gro -s Lconfiguration.

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