gneighbor: print the Gaussian neighborhood values for residue in a protein

gneighbor [ -p probe-radius ] [ -s sigma ] [ input-file ]

The gneighbor command reads the input Protein Data Bank format file (or standard input if omitted), and, assuming file contains the the atomic coordinates of a protein, computes and prints the Gaussian neighborhood values of each residue to standard output. The default values for the probe radius and sigma are 1.5 and 1.5 respectively; these values may be changed using the -p and -s flags.

Note: The Gaussian neighborhood values should be calculated for molecules with all atoms present. In particular, hydrogens must be added if they are missing.

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