García-García C, Draper DE. Electrostatic interactions in a peptide-RNA complex. Journal of Molecular Biology. 331 (1), 75-88, 2003. http://dx.doi.org/10.1016/S0022-2836(03)00615-6

with the minimized PDB files kindly provided by David Draper. It uses the change in binding free energy with ionic strength to estimate the change in number of ions "bound" (diffusively) to RNA upon protein binding.

A more comprehensive walkthrough of this example is available online.

The APBS results agree reasonably well with Draper's calculations; there are some differences in parameterization, surface definitions, etc. that lead to small differents in the results.

To run this example, make sure that the apbs and dxmath binaries are in your path; e.g.,

export PATH=/path/to/apbs/executable:$PATH
export PATH=/path/to/tools/dxmath/executable:$PATH

|APBS Version|Input file|APBS Result| |---|---|---| |3.0 |apbs-0.025.in|8.674116429351E+01 | |apbs-0.050.in| 9.606836713867E+01 | |apbs-0.075.in| 1.011537214883E+02 | |apbs-0.100.in| 1.046142116108E+02 | |apbs-0.125.in| 1.072226817611E+02 | |apbs-0.150.in| 1.093084123761E+02 | |apbs-0.175.in| 1.110412443877E+02 | |apbs-0.200.in| 1.125199716537E+02 | |apbs-0.225.in| 1.138070465620E+02 | |apbs-0.250.in| 1.149444369078E+02 | |apbs-0.275.in| 1.159616972338E+02 | |apbs-0.300.in| 1.168804254687E+02 | |apbs-0.325.in| 1.177168854907E+02 | |apbs-0.400.in| 1.198456038802E+02 | |apbs-0.500.in| 1.220607673699E+02 | |apbs-0.600.in| 1.238080564885E+02 | |apbs-0.700.in| 1.252364090877E+02 | |apbs-0.800.in| 1.264340604647E+02 |1.5 |apbs-0.025.in|8.674120000000e+01 | |apbs-0.050.in|9.606840000000e+01 | |apbs-0.075.in|1.011540000000e+02 | |apbs-0.100.in|1.046140000000e+02 | |apbs-0.125.in|1.072230000000e+02 | |apbs-0.150.in|1.093080000000e+02 | |apbs-0.175.in|1.110410000000e+02 | |apbs-0.200.in|1.125200000000e+02 | |apbs-0.225.in|1.138070000000e+02 | |apbs-0.250.in|1.149440000000e+02 | |apbs-0.275.in|1.159620000000e+02 | |apbs-0.300.in|1.168800000000e+02 | |apbs-0.325.in|1.177170000000e+02 | |apbs-0.400.in|1.198460000000e+02 | |apbs-0.500.in|1.220610000000e+02 | |apbs-0.600.in|1.238080000000e+02 | |apbs-0.700.in|1.252360000000e+02 | |apbs-0.800.in|1.264340000000e+02 |1.4.2 |apbs-0.025.in|8.674120000000e+01 | |apbs-0.050.in|9.606840000000e+01 | |apbs-0.075.in|1.011540000000e+02 | |apbs-0.100.in|1.046140000000e+02 | |apbs-0.125.in|1.072230000000e+02 | |apbs-0.150.in|1.093080000000e+02 | |apbs-0.175.in|1.110410000000e+02 | |apbs-0.200.in|1.125200000000e+02 | |apbs-0.225.in|1.138070000000e+02 | |apbs-0.250.in|1.149440000000e+02 | |apbs-0.275.in|1.159620000000e+02 | |apbs-0.300.in|1.168800000000e+02 | |apbs-0.325.in|1.177170000000e+02 | |apbs-0.400.in|1.198460000000e+02 | |apbs-0.500.in|1.220610000000e+02 | |apbs-0.600.in|1.238080000000e+02 | |apbs-0.700.in|1.252360000000e+02 | |apbs-0.800.in|1.264340000000e+02 Please see the ChangeLog or the [APBS website](http://www.poissonboltzmann.org/) for more information.