g2spinach.m
Makes Spinach data structures from parsed outputs of electronic structure theory packages, such as Gaussian and ORCA. This function converts the information obtained by parsing an electronic structure theory log file into the form that Spinach gateway function create.m understands.
Syntax
[sys,inter]=g2spinach(props,particles,references,options)
Parameters
props - the output of gparse.m function particles - a cell array of the following form: {{'H','1H'},{'N','15N'}...} giving the list of elements and isotopes that should be imported; all other spins will be ignored. If the isotope list contains an electron, e.g. {{'E','E'},{'H','1H'}...}, then EPR mode is assumed - chemical shielding and scalar couplings are ignored, but g-tensor and hyperfine couplings are included. references - a vector of absolute shielding values for the reference substances that are to be placed at zero ppm chemical shift; you ne- ed to run separate electronic structure theory calculations for those substances wuth the same method. Absolute isotropic shielding values for tetramethylsilane in vacuum are: GIAO 13C 1H B3LYP/6-31G* 189.6621 32.1833 B3LYP/6-311+G(2d,p) 182.4485 31.8201 HF/6-31G* 199.9711 32.5957 HF/6-311+G(2d,p) 192.5828 32.0710 CSGT 13C 1H B3LYP/6-31G* 188.5603 29.1952 B3LYP/6-311+G(2d,p) 182.1386 31.7788 HF/6-31G* 196.8670 29.5517 HF/6-311+G(2d,p) 192.5701 31.5989 This setting is ignored when electrons are present in the system. options.min_j - scalar coupling threshold in Hz. J-coup- lings smaller than this value will be ignored in the NMR mode. options.min_hfc - hyperfine coupling threshold in Hz. Hy- perfine tensors with a Frobenius norm smaller than this value will be ignored in the EPR mode. options.purge - if set to 'on' in EPR mode, removes the spins with hyperfine coupling below options.min_hfc from the spin system. options.no_xyz - if set to 1, causes the function to ig- nore the coordinate information and only keep the interaction tensors
Returns
The following subfields of sys and inter data structures are set by this function:
sys.isotopes - Nspins x 1 cell array of strings
inter.coordinates - Nspins x 3 dense matrix, Angstrom. Not
returned if there is an electron in the
isotope list (in the EPR case it is not
a good idea to use the molecular
coordinates for spins).
inter.zeeman.matrix - Nspins x 1 cell array of 3x3 matrices,
ppm for nuclei, g-tensor for electrons.
Zero interactions have zero matrices.
inter.coupling.matrix - Nspins x Nspins cell array of 3x3 matrices,
all in Hz. Zero interactions have zero
matrices.
inter.coupling.scalar - Nspins x Nspins cell array of scalar
couplings, all in Hz. Zero couplings are
returned as zeros.
inter.spinrot.matrix - spin-rotation coupling tensors for
each nucleus
Examples
A typical example of a Spinach input that uses data import from a Gaussian log appears below.
% Read the spin system properties (vacuum DFT calculation)
options.min_j=1.0;
[sys,inter]=g2spinach(gparse('../standard_systems/sucrose.log'),{ {'H','1H'} },31.8,options);
% Magnet field
sys.magnet=14.1;
% Basis set
bas.formalism='sphten-liouv';
bas.approximation='IK-2';
bas.connectivity='scalar_couplings';
bas.prox_level=2;
% Relaxation theory parameters
inter.relaxation={'redfield'};
inter.rlx_keep='secular';
inter.tau_c=1e-9;
% Spinach housekeeping
spin_system=create(sys,inter);
spin_system=basis(spin_system,bas);
% Sequence parameters
parameters.spins={'1H'};
parameters.rho0=state(spin_system,'L+','1H','cheap');
parameters.coil=state(spin_system,'L+','1H','cheap');
parameters.decouple={};
parameters.offset=1800;
parameters.sweep=5000;
parameters.npoints=8192;
parameters.zerofill=65536;
parameters.axis_units='ppm';
parameters.invert_axis=1;
% Simulation
fid=liquid(spin_system,@acquire,parameters,'nmr');
% Apodization
fid=apodization(fid,'crisp-1d');
% Fourier transform
spectrum=fftshift(fft(fid,parameters.zerofill));
% Plotting
plot_1d(spin_system,real(spectrum),parameters);
Further examples of Gaussian inputs: gaussian_a.txt, gaussian_b.txt, gaussian_c.txt - note that the extra printing flag (#p) should always be present.
Notes
As a reference, here are absolute isotropic shielding values for TMS in vacuum:
GIAO 13C 1H
B3LYP/6-31G* 189.6621 32.1833
B3LYP/6-311+G(2d,p) 182.4485 31.8201
HF/6-31G* 199.9711 32.5957
HF/6-311+G(2d,p) 192.5828 32.0710
CSGT 13C 1H
B3LYP/6-31G* 188.5603 29.1952
B3LYP/6-311+G(2d,p) 182.1386 31.7788
HF/6-31G* 196.8670 29.5517
HF/6-311+G(2d,p) 192.5701 31.5989
For chemical shift tensors, the anisotropies computed with electronic structure methods (DFT, MP2, etc.) are usually satisfactory for the purposes of relaxation theory, but the isotropic chemical shifts can differ significantly from the experimental values. After the import is complete, the isotropic parts of chemical shift tensors may be replaced with their experimental values using shift_iso.m function.
See also
gparse.m, oparse.m, create.m, shift_iso.m, c2spinach.m, cyprinol.m, fatty_acid.m, gissmo2spinach.m, karplus_fit.m, killcross.m, killdiag.m, merge_inp.m, methyl_group.m, nuclacid.m, ocparse.m, parsexml.m, protein.m, read_bmrb.m, read_pdb_nuc.m, read_pdb_pro.m, v2spinach.m, weblab2nqi.m, x2spinach.m, Import,_export,_and_visualisation
Version 1.9, authors: Ilya Kuprov
