[gmx-users] Parametrisation of the heteroatomic pdb

James Starlight jmsstarlight at gmail.com
Thu Nov 10 19:50:09 CET 2011

Thomas, thank you!

It's my inattention so I've missed DALA in the rtp file :(

So as I've understood the difference just in one string
 CA     N     C    CB     gi_2   for L form
CB     N     C    CA     gi_2  for D form


2011/11/10 Thomas Piggot <t.piggot at soton.ac.uk>

> 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<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 <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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