The example input files in this directory simulate the binding of various (small) ligands to FKBP. Analogous to HCA binding case (except it works).
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:
This example was contributed by Jung-Hsin Lin.
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 | 0.5.1 | 15.0089 | 19.097 |
0.5.0 | 15.0089 | |||
0.4.0 | 15.0089 | |||
1d7h-dmso/apbs-smol.in | 1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm smol | 0.5.1 | 16.2458 | 19.097 |
0.5.0 | 16.2458 | |||
0.4.0 | 16.24581 | |||
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 | 0.5.1 | 14.4254 | 16.231 |
0.5.0 | 14.4254 | |||
0.4.0 | 14.4254 | |||
1d7i-dss/apbs-smol.in | 1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm smol | 0.5.1 | 15.4517 | 16.231 |
0.5.0 | 15.4517 | |||
0.4.0 | 15.45171 | |||
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: