[gmx-users] back calculation of NOE:s

[Anton Feenstra]

David van der Spoel wrote:
> On Thu, 2003-07-31 at 11:43, Jonas Fast wrote:
>>As a beginner with gromacs and structure calculations, I have used gromacs
>>to get the structure of a protein bound fatty acid from NOE data (only using
>>the internal fatty acid NOE:s to get distance restraints). Now I would like
>>to check the result by back calculating a noesy spectra. Could somebody line
>>up a feasible pathway for that together with suitable software tips. I am at
>>the state where I have made a successful (?) full MD simulation of the
>>system (fa, water and sodium as a counter ion).
> 
> this is an interesting topic. You may consider to use experimental
> chemical shifts, because calculated ones are not accurate enough,
> however it would also be interesting to compute chemical shifts (using
> David Case's programs) and then build up a spectrum like that. The
> intensity of the NOE's is proportional to 
> sigma = r^6

Well, only to a rather crude approximation. If you already have the simulations,
you can do much better by taking the proton pair spectral density functions
from the distance (auto)correlations, and then integrate the relaxation matrix
to the appropriate mixing time. If you're still with me, you may want to read
some of Christine Peter's papers (Wilfred van Gunsteren's group , ETH Zurich).
She also analyzed some of my peptide simulations, so I could compare them to
my NMR experiments. The corresponding paper is: J. Biomol. NMR 23, 181-194, 2002
(there is a .pdf of it on my homepage at http://www.few.vu.nl/~feenstra/ ).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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