surf

Calculate the LCPO surface area of specified atoms. Can do partial surface areas.

surf [<name>] [<mask1>] [out <filename>] [solutemask <mask>] [offset <offset>] [nbrcut <cut>]

<name> Output data set name.
<mask1> Atoms to calculate surface area for.
out <filename> File to write surface area to.
solutemask <mask> If specified, calculate the contribution of <mask1> to <mask>.
offset <offset> Increment van der Waals radii by <offset>; 1.4 Ang. is the default (as used by Amber).
nbrcut <cut> Only atoms with van der Waals radii greater than <cut> are considered to have neighbors (2.5 Ang Amber default).

Calculate the surface area in of atoms in <mask> (all solute atoms if no mask specified) using the LCPO algorithm of Weiser et al. In order for this to work, the topology needs to have bond information and atom type information. Note that even if does not include all solute atoms, the neighbor list is still calculated for all solute atoms so the surface area calculated reflects the contribution of atoms in to the overall surface area, not the surface area of as an isolated system. As a result, it may be possible to obtain a negative surface area if only a small fraction of the solute is selected.

Note that even if <mask> does not include all solute atoms, the neighbor list is still calculated for all solute atoms so the surface area calculated reflects the contribution of atoms in <mask> to the overall surface area, not the surface area of <mask> as an isolated system. As a result, it may be possible to obtain a negative surface area
if only a small fraction of the solute is selected.

For example, to calculate the overall surface area of all solute atoms, as well as the contribution of residue 1 to the overall surface area, writing both results to surf.dat:

surf out surf.dat
surf :1 out surf.dat