Karplus fit.m

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Fits a Karplus curve to a Gaussian dihedral angle scan.

Syntax

    [A,B,C]=karplus_fit(dir_path,atoms)

Description

This function scans the user-supplied directory for Gaussian calculation logs, reads the ones it can find, extracts the dihedral angles and the J-couplings between the specified atoms, and fits the Karplus formula to that data. The directory specified should contain a series of Gaussian J-coupling calculation logs that differ only in the value of the dihedral angle in question.

Arguments

    dir_path - the path to the directory containing Gaussian logs
    atoms    - a four-element vector containing the numbers of the 
               atoms that make up the dihedral angle. The coupling
               is between the atoms specified in the first and the
               last element.

Returns

    [A,B,C]  - the three coefficients in the following equation:
                 
                      J(phi)=A*cos(phi)^2+B*cos(phi)+C

Examples

The following figure is returned by /examples/nmr_proteins/karplus_extract.m example file:

Karplus fit.png

The probability histogram is dominated by a single block due to the presence of a strong hydrogen bond.

Notes

Karplus curves are used extensively by the J-coupling guesser functions guess_j_pro.m and guess_j_nuc.m in the biomolecular NMR module.

See also

guess_j_pro.m, guess_j_nuc.m


Revision 3284, authors: Ilya Kuprov