deletions | additions       diff --git a/subsection_NMR_calculations_and_protein__.tex b/subsection_NMR_calculations_and_protein__.tex  index 2e17eb9..5b43edb 100644  --- a/subsection_NMR_calculations_and_protein__.tex  +++ b/subsection_NMR_calculations_and_protein__.tex 
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\subsection{NMR calculations and protein structures used}  In this paper we benchmark the NMR chemical shift predictions on ubiqutin and Protein G. The structures are geometry optimized using PM6-D3H+ using the PCM solvation model and the CHARMM22/CMAP force field using the xx solvation model using the 1UBQ and 2OED crystal structures as starting points. The PM6-D3H+ optimizations are done using the GAMESS program and a convergence criterion of 5x10^{-4} 5 x 10^{-4}  atomic units, while the CHARMM22/CMAP optimizations are done using TINKER xx? with an convergence criterion of xx. In addition the following NMR-derived structural ensembles are used without further refinement: 1D3Z, 2K39, 1XQQ, 2LJ5, 2KOX. In all calculation we used charged protonation states for the acidic and basic side chains (also His xx?). OBPE/6-31G(d,p)//PM6-D3H+ GIAO NMR shielding calculations are performed with Gaussian09 using the PCM solvation model. ProCS15 chemical shielding calculations are performed using ... CheShift-2 calculations are performed using .. CamShift, ppmone,Sparta+, Shaic, and ShiftX2 calculations are performed using stand-alone codes downloaded and installed on a local cluster. The NMR chemical shielding and shifts are compared to shifts measured by xx and xx for 1UBQ and 2OED, respectively. Much of the variation in some of the chemical shifts comes from the nature of the side-chain itself and the side chains before and after in the sequence, which can lead to inflated R values. To separate the contributions of the sequence and the structure we subtract the measured sequence corrected random coil values (xx) from all predicted and experimental values. Note that this does not affect the computed RMSD values.  
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