# Karplus fit.m

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:

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.