Re: AMBER: Chemical shift: simulation vs. experiment

From: Mingfeng Yang <>
Date: Thu, 3 May 2007 22:16:30 -0700

Emmm. I am gotta reply to myself.

I guess the under-estimate of backbone N chemical shift must due to the
fact that N-H can't form hydrogen bond with water in implicit solvent. Am I

Anyway, it's pretty exciting to see that simulation can reproduce
experimental values so well.

On 5/3/07, Mingfeng Yang <> wrote:
> Dear fellows,
> This topic might not be so relevant to Amber. But I do need a little
> help from our community, since I can barely find anyone to discuss with
> me right now.
> I finished a MD simulation done by Amber9, igb=7, PARM99SB force fields,
> and tried to compare the results with experiment. Below is what I did:
> I took an ensemble average of the chemical shift values of N, CA, CB
> which were calculated by Dr. Case's SHIFTS program, and compared with
> the corresponding chemical shifts determined by solution state NMR.
> Encouragingly, for CA and CB atoms, the correlations between simulation
> and experiment are nearly 1 (>0.995). The correlation for N atoms are
> 0.877 which I consider still pretty decent, but the N chemical shifts
> are smaller than experimental values by 5.
> Can anybody explain the difference of N chemical shifts between
> simulation and experiments?
> Do you consider the comparison fair, and the results be encouraging?
> Thanks,
> Mingfeng
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Received on Sun May 06 2007 - 06:07:25 PDT
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