[gmx-users] back calculation of NOE:s

[David van der Spoel]

On Thu, 2003-07-31 at 11:43, Jonas Fast wrote:
> Dear gmx-users!
> 
> 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).
> 
> Thanks!
> 

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

The g_disre program will compute the distances with appropriate
weighting for you. If you decide to use epxerimental shifts you then
only have to combine the shifts data with the inversed distances to get
the NOE spectrum


> Best regards
> 
> Jonas
> 
> *********************************************************
> Jonas Fast, PhD student
> Department of Biophysical Chemistry
> Lund University, Box 124
> SE-22100 LUND, Sweden
> Phone: +46 - 46 222 8243
> Fax:   +46 - 46 222 4543
> Mobile:+ 46 701 728872
> Email: jonas.fast at bpc.lu.se
> http://www.bpc.lu.se
> *********************************************************
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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