Jan Jensen edited subsection_QM_NMR_calculations_on__.tex  almost 9 years ago

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\subsection{QM NMR calculations on full proteins}  In the following sections ProCS14 is benchmarked on QM NMR calculations on full protein models. The proteins are a crystal structure of ubiquitin(1UBQ) with 76 residues and two models of Protein G, 2OED\cite{2oed} which is a crystal structure refined with dipolar couplings and 1IGD\cite{1igd} the crystal structure of protein G. The protonation states of LYS, ARG, HIS, GLU and ASP is if necessary changed to the same as in ProCS14. The QM NMR calculations is done on both the unmodified crystal structures and optimized versions. PM6 was used in order to get an optimized structure with approximately the same bond angles and bond lengths as  the tripeptides. The PM6-D3H+\cite{dh3plus} with a PCM model was used and PM6-DH+\cite{pm6dh} with the COSMO solvation model. Pure PM6 was not able to converge most likely because it lacks the dispersion and hydrogen bonding corrections of PM6-D3H+ and PM6-DH. In addition to PM6 the proteins was also optimized with a selection of forcefields, AMBER\cite{amber}, CHARMM22/CMAP\cite{CHARMM2009} and AMOEBAPRO13\cite{AMOEBA}. The NMR calculations were done at the GIAO OPBE/6-31G(d,p) PCM level of theory in Gaussian 09.