Re: AMBER: Chemical shift: simulation vs. experiment

From: Adrian Roitberg <>
Date: Fri, 04 May 2007 08:42:55 +0200

Dear Mingfeng,
N (of Amide) chemical shifts should be around 120, but some range of
maybe 20 to 30. Do you mean that your N shifts from the program are
around 25 ? That would make them 5 times smaller then experiment.

Please clarify.
We can N shifts around 120 for amide N using the same setup. As
mentioned H-amide chemical shifts are much harder. Doing the simulation
in real water does not help either, because shifts does not really look
at the waters when doing the calculation, so you are still missing the
effect of charges.


Mingfeng Yang wrote:
> 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
> right?
> Anyway, it's pretty exciting to see that simulation can reproduce
> experimental values so well.

>> 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.
but the N chemical shifts
>> are smaller than experimental values by 5.

                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email
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Received on Sun May 06 2007 - 06:07:25 PDT
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