Automatic fragmentation (AFNMR) program for calculating chemical shifts
Tong Zhu, Xiao He, Jason Swails and David A. Case
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Full instructions are in the doc/afnmr.pdf file
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License information is in the LICENSE file
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For the impatient: 'make install && make test'
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Best papers to read/cite:
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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).
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D.A. Case. Using quantum chemistry to estimate chemical shifts in biomolecules. Biophys. Chem. 267, 106476 (2020).
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Version history:
- Version 1.0 is the initial split from the "shifts" code base
- Version 1.1 makes 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 jaguar, plus other small tweaks
- Version 1.5 provides for fixes for non-sequential residue numbers, adds tweaks for quantum geometry optimization
- Version 1.6 fixes a bug in how the external charges were written for ORCA
- Version 1.6.1 fixes a mistake in the documentation about the -mol2 flag; tweaks for handling extra points
- Version 1.7 is a significant update: incorporating pcS-seg2 basis, new mixed basis, tweaked fragmentation.
- Version 1.8 add support for spin-spin couplings, updates to xtb optimization
- Version 1.9 increases the cutoff for protein-water interactions; allows xtb optimization to go to completion or 500 cycles