The afnmr suite allows one to estimate chemical shifts in
biomoleucles, based on a fragmentation approach, and quantum chemical
calculations. This functionality
is self-contained and does not require
The basic ideas are presented in the
- X. He, B. Wang, and K.M. Merz, Jr. Protein NMR Chemical Shift Calculations
Based on the Automated Fragmentation QM/MM Approach. J. Phys. Chem. B
113, 10380-10388 (2009).
- T. Zhu, X. He, and J.Z.H. Zhang. Fragment density functional theory
calculation of NMR chemical shifts for proteins with implicit solvation. Phys.
Chem. Chem. Phys. 14, 7837-7845 (2012)
- T. Zhu, J.Z.H. Zhang, and X. He. Automated Fragmentation QM/MM Calculation
of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. J.
Chem. Theory Comput. 9, 2104-2114 (2013)
- S. Tang and D.A. Case. Calculation of chemical shift anisotropy in
proteins. J. Biomol. NMR 51, 303-312 (2011).
- D.A. Case. Chemical shifts in biomolecules. Curr. Opin. Struct. Biol.
23, 172-176 (2013).
- J. Swails, T. Zhu, X. He and David A. Case. AFNMR: Automated fragmentation
quantum mechanical calculation of NMR chemical shifts for biomolecules.
J. Biomol. NMR 63, 125-139 (2015).
- D.A. Case. Using quantum chemistry to estimate chemical shifts
in biomolecules. Biophys. Chem. 267, 106476 (2020).
Here are some recent applications:
- H. Zhang, G. Hou, M. Lu, J. Ahn, I.-J. Byeon, C.J. Langmead, J.R.
Perilla, I. Hung, P.L. Gor'kov, Z. Gan, W. Brey, D.A. Case, K. Schulten, A.M.
Gronenborn, and T. Polenova. HIV-1 Capsid Function is Regulated by Dynamics:
Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning
NMR, QM/MM, and MD. J. Am. Chem. Soc. 138, 14066-14075 (2016).
- M. Fritz, C.M. Quinn, M. Wang, G. Hou, X. Lu, L.M.I. Koharudin, J.
Struppe, D.A. Case, T. Polenova and A.M. Gronenborn. Accurate determination of
backbone chemical shift tensors in microcrystalline proteins by integrated MAS
NMR and QM/MM. Phys. Chem. Chem. Phys. 20, 9543-9553 (2018).
- H. Shi, M.C. Clay, A. Rangadurai, B. Sathyamoorthy, D.A. Case, and
H.M. Al-Hashimi. Atomic Structures of Excited State A-T Hoogsteen Base Pairs
in Duplex DNA by Combining NMR Relaxation Dispersion, Mutagenesis, and
Chemical Shift Calculations. J. Biomol. NMR 70, 229-244 (2018).
- H. Zhou, B. Sathyamoorthy, A. Stelling, Y. Xu, Y. Xue, Y.Z.
Pigli, D.A. Case, P.A. Rice, and H.M. Al-Hashimi. Characterizing
Watson–Crick versus Hoogsteen Base Pairing in a DNA–Protein Complex
Using Nuclear Magnetic Resonance and Site-Specifically 13C-and
15N-Labeled DNA. Biochemistry 58, 1963-1974 (2019).
- H. Shi, A. Rangadurai, H.A. Assi, R. Roy, D.A. Case, D.
Herschlag, J.D. Yesselman, and H.M. Al-Hashimi. Rapid and accurate
determination of atomistic RNA dynamic ensemble models using NMR and
structure prediction. Nature Commun. 11, 5531 (2020).
The latest version (1.6, September, 2022) of the afnmr package
can be obtained from:
Installation and usage instructions are in the afnmr.pdf file, in the
"doc" folder. As noted above, afnmr is fully self-contained, and
does not require AmberTools.
Version 1.1 is a minor update from version 1.0, mainly making it easier
to use snapshots for solvated molecular dynamics simulations as inputs.
Version 1.2 is the first to be hosted on github, and changes the
default basis to pcSseg-0. Version 1.3 updates the way in which
reference shieldings are estimated, using DFT calculations on reference
compounds. Version 1.3.1 fixes the ways in which waters and ligands are
handled. Version 1.4 adds support for the jaguar program. Version 1.5
allows for non-consecutive residue numbers, and tweaks the initial
optimization. Version 1.6 fixes a bug in how external charges were
written for ORCA.
Updated on December 1, 2022. Comments to firstname.lastname@example.org