AMBER Archive (2006)

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

From: thenmalar (thenmalar_at_ibab.ac.in)
Date: Wed Mar 01 2006 - 16:01:52 CST

Dear Ambers,
   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. I will be thankful if someone can
share their views about this discrepency.
  However, if I want to use both N-H and C-H data sets to refine my NMR
structure using amber, am I have to treat them as different data sets.

Thank you in advance,
Thenmalar
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