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] =