Quantum chemical estimates chemical shifts in proteins and nucleic acids

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 AmberTools.

The basic ideas are presented in the following papers:

  1. 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).

  2. 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)

  3. 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)

  4. S. Tang and D.A. Case. Calculation of chemical shift anisotropy in proteins. J. Biomol. NMR 51, 303-312 (2011).

  5. D.A. Case. Chemical shifts in biomolecules. Curr. Opin. Struct. Biol. 23, 172-176 (2013).

  6. 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).

  7. D.A. Case. Using quantum chemistry to estimate chemical shifts in biomolecules. Biophys. Chem. 267, 106476 (2020).

Here are some recent applications:

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 April 10, 2023. Comments to david.case@rutgers.edu