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

[Christian Blau]

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
>