There are tons of Carbon shifts in BMRB.
But... be aware that mapping the naming. etc from BMRB to the same
protein the pdb, is not as trivial as one would hope.
adrian
On 2/13/20 11:05 AM, Lod King wrote:
> [External Email]
>
> thank you for your email.
> I only found the NMR values for proton, and limited carbon data there.
> I have seen people use sparta+ to calculate, I would give a try.
>
> On Thu, Feb 13, 2020 at 7:08 AM Gordon Richard Chalmers <gordoncs.uga.edu>
> wrote:
>
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__casegroup.rutgers.edu_&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=_lCysk2d4tsZPBPr_8T3xE_qjhM4QRfvMWriVhI2QAo&s=gd1WvrV8bBNX2T6gpqn4ANKyhADxilIUFiVmQwv4Sis&e=
>> 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.
>>> _______________________________________________
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>>>
>>
>> --
>> -----------------------------------------------------------------
>> Christina Bergonzo
>> Research Chemist
>> Biomolecular Measurement Division, MML, NIST
>> -----------------------------------------------------------------
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Feb 13 2020 - 08:30:01 PST
