[gmx-users] Calculate NMR shift from simulation

[Andrea Spitaleri]

Hi,
this task is quite challenging and up to now there are few valid protocols to quantitative correlate simulations with chemical shift calculations. Moreover you are dealing with chemical shift perturbation calculation, I mean the chemical shift variation due to either the dynamics of the system or binding of a ligand or like in your case the change of solvent. In the first case from NMR you get only the average and the correlation is hard to get with MD. 

As I said, you can have look to these software to calcualate a posteriori (scripting ...) the chemical shift:

http://shiftx.wishartlab.com/
http://www.shiftx2.ca/
http://casegroup.rutgers.edu/qshifts/about.htm
http://spin.niddk.nih.gov/bax/software/SPARTA+/
https://www.shef.ac.uk/mbb/staff/williamson/shifts

Based on the last approach, you can read these papers to get more details, where the chemical shifts are studied on different solvents:

http://pubs.acs.org/doi/abs/10.1021/jm701194r
http://pubs.rsc.org/en/Content/ArticleLanding/2012/CE/C2CE25941A#!divAbstract
http://pubs.rsc.org/en/Content/ArticleLanding/2004/CE/b407163h#!divAbstract

HTH

Best

and


________________________________
Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html

ORCID: http://orcid.org/0000-0003-3012-3557


________________________________________
Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] per conto di Tushar Ranjan Moharana [tusharranjanmoharana at gmail.com]
Inviato: martedì 29 dicembre 2015 9.42
A: gromacs.org_gmx-users at maillist.sys.kth.se
Oggetto: [gmx-users] Calculate NMR shift from simulation

Hi everyone ,
I have the shift in peak of amide proton and amide nitrogen of my protein
in various polar organic solvent (40% solvent and rest water). I have
simulated the protein in same condition. There is no major structural
difference observed both by CD (ellipticity) and by simulation. The shift
in peak is of the order of .5 ppm for proton and 2 ppm for nitrogen (pure
water vs 40% solvent). Can anybody suggest me how to correlate my
simulation and observed shift? I mean which parameter I should calculate?

I have calculated difference in hydrogen bonding (pure water vs 40%
solvent) also number of solvent molecule within 0.4 nm. However nothing
correlated with observed shift (correlation coefficient less than 0.02).

Any advice is precious and I am thankful for the same.



"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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