[gmx-users] Parametrisation of the heteroatomic pdb
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.
> James Starlight wrote:
>> 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 <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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