[gmx-users] Parametrisation of the heteroatomic pdb

Thomas Piggot t.piggot at soton.ac.uk
Thu Nov 10 17:17:14 CET 2011

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.



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.

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