Calculate Connolly surface area of specified atoms.

molsurf [<name>] [<mask>] [out filename] [probe <probe_rad>] [radii {gb | parse | vdw}] [offset <rad_offset>]

[<name>] Name of surface area data set.
[<mask>] Atoms to calculate surface area of.
[out <filename>] File to write values to.
[probe <probe_rad>] Probe radius (default 1.4 Angstrom).
[offset <rad_offset>] Add <rad_offset> to each atom radius (default 0.0).
[radii {gb|parse|vdw}] Specify radii to use: gb GB radii (default). parse PARSE radii. vdw van der Waals radii.

Calculate the Connolly surface area of atoms in <mask> (default all atoms if no mask specified) using routines from molsurf (originally developed by Paul Beroza) using the probe radius specified by probe (1.4 Å if not specified). Note that if GB/VDW radii are not present in the topology file (e.g. for PDB files), then PARSE radii can be used. Also note that this routine only calculate absolute surface areas, i.e. it cannot be used to get the contribution of a subset of atoms to overall surface area; if such functionality is needed try the surf command.