AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 01 2006 - 16:38:09 CST

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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