[gmx-users] Chemical Shifts prediction using gmx chi -shift

[Florent Langenfeld]

Dear Christian,

Thanks for your answer.

Correct me if I'm wrong: the **-shift.dat grids contain chemical shift deviations compared to a set
of reference (amino-acid-dependent) chemical shifts (taken from table 2 of "D. S. Wishart and A. M. Nip, Protein
Chemical Shift Analysis: A Practical Guide, Biochem. Cell Biol., 76, 1998, 153-163), and these deviations
are picked up according to the phi-psi angle of each residue (there are 18 rows and columns in the grid files,
so my guess is that dihedral angles are binned according to a 20° scheme), for each frame of the trajectory.

The final result is then the mean of the deviations for each chemical shift considered (Ca, Ha, CO and Cb).

In the paper you cite, I cannot find the reference value for Alanine and Tyrosine residues;
so I am wondering where the reference values for these residues come from.

Thanks again for your help!

Best,

Florent

> Hello Florent,
>
>
> The tool is based on? "D. S. Wishart and A. M. Nip", "Protein Chemical Shift Analysis: A Practical Guide", "Biochem.
> Cell Biol.", 76, 1998, "153-163"
>
> It reads chemical shift reference data on a phi-psi-angle grid from ca-shift.dat, cb-shift.dat, ha-shift.dat and
> co-shift.dat. The tool interpolates this data for the respective angle and sums it up. This sum is then normalized by
> the number of trajectory frames.
>
>
> Best,
>
> Christian
>
>
> On 2019-12-06 17:39, Florent wrote:
>> Dear users,
>>
>>
>> I recently tried to use the -shift option of gmx chi, and I'm a bit confused about two things:
>>
>> 1) How does gromacs generate these results (chemical shift deviations from reference values)? The command-line
>> documentation is of little help ("Compute chemical shifts from phi/psi angles")...
>>
>> 2) What are the reference values for Alanine and Tyrosine residues from? The calculation generates a log with a
>> reference (Protein Chemical Shift Analysis: A Practical Guide), that does not contain any value for Alanine and
>> Tyrosine residues while chemical shifts deviations are computed for those residues...
>>
>>
>> Any help or reference to a more complete documentation would be appreciated.
>>
>>
>> Best,
>>
>>
>> Florent
>>
>