[gmx-users] Parametrisation of the heteroatomic pdb

[Thomas Piggot]

Hi James,

I suggest to see the differences in topologies for L and D amino acids 
(in the GROMOS force fields at least) you look in the aminoacids.rtp 
file and in particular the differences between the ALA and DALA entries.

Cheers

Tom

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  
> 
> 
> 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 ?
> 
> 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.
> 
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.