In order to calculate solvation energy upon binding you will need to take the results from these input files and subtract from them the results obtained from the coulomb
utility found at apbs/tools/manip/coulomb
. The values returned from this utility are:
Input File | Description | APBS Version | Results (kJ/mol) | UHBD (kJ/mol) |
---|---|---|---|---|
1d7h-dmso/apbs-mol.in | 1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm mol | 0.4.0 | 15.0089 | 19.097 |
1d7h-dmso/apbs-smol.in | 1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm smol | 0.4.0 | 16.24581 | 19.097 |
0.3.2 | 15.0089 | |||
0.3.1 | 15.0089 | |||
0.3.0 | 15.0089 | |||
0.2.6 | 15.0089 | |||
0.2.5 | 15.0089 | |||
0.2.4 | 15.0089 | |||
0.2.3 | 15.0097 | |||
0.2.2 | 14.5886 | |||
0.2.1 | 14.589 | |||
0.2.0 | 14.589 | |||
0.1.8 | 14.591 | |||
1d7i-dss/apbs-mol.in | 1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm mol | 0.4.0 | 14.4254 | 16.231 |
1d7i-dss/apbs-smol.in | 1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm smol | 0.4.0 | 15.45171 | 16.231 |
0.3.2 | 14.4254 | |||
0.3.1 | 14.4254 | |||
0.3.0 | 14.4254 | |||
0.2.6 | 14.4254 | |||
0.2.5 | 14.4254 | |||
0.2.4 | 14.4254 | |||
0.2.3 | 14.4254 | |||
0.2.2 | 14.3865 | |||
0.2.1 | 14.387 | |||
0.2.0 | 14.387 | |||
0.1.8 | 15.210 |
1 The discrepancy in values between versions 0.4.0 and 0.3.2 is most likely due to three factors:
Please see the ChangeLog or the APBS documentation for more information.