AMBER Archive (2006)

Subject: Re: AMBER: N-H and C-H Residual Dipolar Coupling

From: thenmalar (
Date: Wed Mar 01 2006 - 18:59:34 CST

Dear Prof. Case,
           Thank you very much for clarifying my doubt.

> On Thu, Mar 02, 2006, thenmalar wrote:
>> I wish to refine a protein structure using N-H and C-H residual
>> dipolar
>> coupling. To start with, I selected a published RDC data of a protein
>> and used SVD method ( written by me using the previously available
>> method of Prof. Prestegard and his coworkers) to calculate the
>> alignment tensor value, which is to be used in AMBER.
>> What I found is, when I use N-H and C-H rdcs separately, the observed
>> and calculated RDC values matches very well. Interestingly, the
>> alignment tensor magnitude is same for these two situations, but, the
>> sign is exactly opposite. However, if I put them together, I got only
>> the N-H values coincide with the observed value, while the calculated
>> C-H rdc has exactly opposite sign with the observed value. One reason I
>> can see is that the gyromagnetic ratio is positive and negative for N&H
>> respectively, while for both C & H it is positive. But, I believe that
>> it should not affect the calculation
> It sounds like you have identified the problem. I don't know why you
> think
> that "it [the sign of the gyromagnetic ratio for N] should not affect the
> calculation" -- it should affect things in exactly the way you describe.
> For example, the Dcalc value from the equation on p. 129 of the Amber
> users'
> manual will change sign if you change sign of gamma-N.
> The literature can be confusing here, because some people treat gamma-N as
> if it were positive. As long as the experiment and calculated values are
> treated in the same manner, things are fine. But it sounds like you may
> be
> using published RDC values that treated gamma-N as positive, but are doing
> an
> Amber calculation that uses the (correct) negative value.
> ...hope this helps...dac
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