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 | 1.4.1-binary | 15.0081 | 19.097 |
1.4 | 15.00814 | |||
1.3 | 15.0077 | |||
1.2.1 | 15.00773 | |||
1.2 | 15.00872 | |||
1.1.0 | 15.0089 | |||
1.0.0 | 15.0089 | |||
0.5.1 | 15.0089 | |||
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 | 1.4.1-binary | 16.2445 | 19.097 |
1.4 | 16.24454 | |||
1.3 | 16.2446 | |||
1.2.1 | 16.24463 | |||
1.2 | 16.24562 | |||
1.1.0 | 16.2458 | |||
1.0.0 | 16.2458 | |||
0.5.1 | 16.2458 | |||
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 | 1.4.1-binary | 14.4250 | 16.231 |
1.4 | 14.4250 | |||
1.3 | 14.4250 | |||
1.2.1 | 14.42503 | |||
1.2 | 14.42532 | |||
1.1.0 | 14.4254 | |||
1.0.0 | 14.4254 | |||
0.5.1 | 14.4254 | |||
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 | 1.4.1-binary | 15.4515 | 16.231 |
1.4 | 15.4515 | |||
1.3 | 15.4515 | |||
1.2.1 | 15.45153 | |||
1.2 | 15.4517 | |||
1.1.0 | 15.4517 | |||
1.0.0 | 15.4517 | |||
0.5.1 | 15.4517 | |||
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:
2 APBS 1.2 has switched the multigrid smoothing algorithm from standard Gauss-Seidel to Gauss-Seidel red/black in order to facilitate parallelization. This switch has caused small differences in individual calculation energies which, when combined to the final answer, create larger errors (up to 0.04%). These errors can be reduced by resetting the APBS error tolerance to 1e-9 or smaller values. For a more detailed explanation, please see here.
3 The discrepancy in values between versions 1.2 and 1.2.1 is most likely due to the following factor(s):
4 The discrepancy in values between versions 1.3 and 1.4 is most likely due to the following factor(s):