[gmx-users] Parametrisation of the heteroatomic pdb

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 10 17:30:50 CET 2011

On 11/11/2011 3:17 AM, Thomas Piggot wrote:
> 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.

Good thought :-) I finally see what my brain was missing - the angle of 
the improper dihedral is signed, and the relevant square is outside the 
brackets so the sign matters. The order in which the atoms are specified 
determines the sign of the angle. So molecules with opposite-sense 
chiral centres do need different topologies.


> 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.

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