[gmx-users] Parametrisation of the heteroatomic pdb
Mark.Abraham at anu.edu.au
Thu Nov 10 17:14:38 CET 2011
On 11/11/2011 3:01 AM, James Starlight wrote:
> 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 :)
> 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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