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://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
> >
>
>
> --
> -----------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> Biomolecular Measurement Division, MML, NIST
> -----------------------------------------------------------------
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Received on Thu Feb 13 2020 - 08:30:01 PST
