Hi
Just a quick reply.
It is possible to download all the chemical shifts for a
particular atom from the BMRB. I once did a statistical
analysis of the chemical shift values of amide protons
in the BMRB for each residue type (I was primarily
interested in PHE but that didn't matter). The distribution
of chemical shift values from the BMRB in general for a
given atom type and residue type is not Gaussian, but
rather multi-modal. This is in general for all atom types,
not just amide protons. There is criticism of correct referencing
and the quality of deposited data in the BMRB, but I
disregarded that.
As far as chemical shift prediction from a trajectory. You
could use either ShiftX2 or ppm_one to average over your
frames (or subset, such as every 100 frames). You have to
prepare a 'model' file in cpptraj, from each of the desired
frames of your trajectory. This is explained in the cpptraj
documentation as well as in these chemical shift prediction
software programs. Then either will give you the average
predicted chemical shift for your atom with a little bit of
statistics from the calculation. There are some differences
about the reliability of chemical shift predictions from these
packages for particular proton types; I can't comment about
the Calpha and Cbeta.
I am at RPI now, but I don't have t my Amber account here yet.
Gordon Chalmers
Center for Biotechnology and Interdisciplinary Studies (CBIS)
Rensselaer Polytechnic Institute (RPI)
Room 3235
Gordon Chalmers
________________________________
From: Christina Bergonzo <cbergonzo.gmail.com>
Sent: Thursday, February 13, 2020 8:50 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] BMRB Chemical shift values
[External Sender]
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 - 07:30:02 PST
