[gmx-users] Parametrisation of the heteroatomic pdb

James Starlight jmsstarlight at gmail.com
Thu Nov 10 17:01:15 CET 2011


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 :)

2011/11/10 Mark Abraham <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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