To run Surface Diver in the interactive mode the user should issue the following command:

surf_diver pqr_file

or, to create upon execution DX formatted files with physicochemical properties:

surf_diver pqr_file –grids

(where pqr_file is the pqr formatted file describing the molecule) and then assign values for all needed parameters using the command line, as presented below:

[user@host example]$ ../surf_diver dummy.pqr

* no input file given, switching to interactive mode …

* enter the name of the APBS dx potential file
* use ‘skip’ to disable this feature
(?) [grid] = potential.dx
* APBS grid 129 x 129 x 129
* APBS grid origin: 10.742500 58.097000 -183.097500
* APBS grid spacing: 0.390625 0.000000 0.000000
* APBS grid spacing: 0.000000 0.390625 0.000000
* APBS grid spacing: 0.000000 0.000000 0.390625
* APBS grid points: 2146689
* APBS grid center: 35.742500 83.097000 -158.097500
* dimensions set to 129 x 129 x 129
* total number of points is 2146689
* centre of geometry (x=39.137785, y=83.007412, z=-156.790469)
* enter the inflation radius [A]
(?) [irad] = 0.0
* inflation radius set to: 0.000000 [A]
* max. dimension is 38.884705 [A]
* enter the value of maximal radius to be used
(?) [rmax] = 20
* rmax set to 20.000000 [A]
* enter the order of spherical functions
(?) [spho] = 32
* enter the number of spherical surfaces
(?) [nsph] = 19
* number of spherical surfaces set to 19
* radial spacing is 1.000000
* APBS grid center: 35.742500 83.097000 -158.097500
* (GC – APBSGC): 3.639274
* APBS grid transformation …
* APBS grid origin after translation: -28.395285 -24.910412 -26.307031
* grid spacing is 0.390625 [A]
* radial spacing is 1.000000
* writting to DX files …
* performing decomposition ……………….
* elapsed time = 186s

* done!

where prompt for the user is denoted with (?) [keyword] =