Synopsis

Volume [-chmsvVy] [--vdW] [-o=0.0] [-p=1.4] file

Description

Calculate the surface area and volume using the GaussVol (default) or Connolly algorithm.

Options

-c, --connolly

Use the Connolly algorithm to compute solvent excluded volume and solvent accessible surface area.

-h, --help

Print command help and exit.

-m, --molecular

For Connolly, compute molecular volume and surface area (instead of SEV/SASA).

-o, --offset=0.0

Add an offset to all atomic radii for GaussVol volume and surface area.

-p, --probe=1.4

For Connolly, set the exclude radius (SASA) or probe radius (molecular surface). Ignored for vdW.

-s, --sigma

Use sigma radii instead of Rmin.

-v, --verbose

Print out all components of volume of molecule and offset.

-V, --version

Print the Force Field X version and exit.

--vdW, --vanDerWaals

For Connolly, compute van der Waals volume and surface area (instead of SEV/SASA)

-y, --includeHydrogen

Include Hydrogen in calculation volume and surface area.

Arguments

file

The atomic coordinate file in PDB or XYZ format.