I'm not sure if your question is how to calculate chemical shifts from your
molecular dynamics simulation or how to find available chemical shift data
in the BMRB, so I'll try and address both:
If you have a PDBID you can search the BMRB by the PDBID, or sometimes the
PDB page will link directly to the BMRB entry for a molecule.
It would also be due diligence to search the PDB for different entries of
the same molecule to see the variety of experimental data for a given
structure (X-ray and NMR data, perhaps from multiple labs if it's a popular
structure to study).
In the BMRB you can find a section labeled "Data sets" which link the raw
data set files, and next to it "Data type" and "Count" which show the types
of shifts (or other data deposited) and how many individual values there
are.
Predicting chemical shifts is not something I have a lot of experience
doing - but I've used shifts from Dave Case's group to calculate hydrogen
shifts with minimal setup & trouble: https://casegroup.rutgers.edu/
If you want to do C, N, or P shifts there may be better or other ways to go
about it - but I don't know them offhand.
Good luck,
Christina
On Wed, Feb 12, 2020 at 6:22 PM Lod King <lodking407.gmail.com> wrote:
> Hi Amber
>
> I would like to compare the chemical shift of alpha carbon and beta carbon
> with experimental value and my MD calculation.
>
> Does anyone do this before and how to find those values from the BMRB
> website with a known ID.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Thu Feb 13 2020 - 06:00:01 PST
