The example input files in this directory calculate the binding of a small molecule (acetazolamide) to a medium-sized protein (human carbonic anhydrase).
The UHBD calculations where performed using a van der Waals surface definition for the dielectric coefficient. This is simulated in the APBS input files by setting srad to 0.0.Input File | Description | APBS Version | Results (kJ/mol) | UHBD (kJ/mol) |
---|---|---|---|---|
apbs-mol.in | 2-level focusing to 0.225 A, VdW surface, srfm mol | 1.3 | -52.4647 | -70.00 |
1.2.1 | -52.4647 | |||
1.2 | -52.46474 | |||
1.1.0 | -52.4669 | |||
1.0.0 | -52.4669 | |||
0.5.1 | -52.46693 | |||
0.5.0 | -52.10622 | |||
0.4.0 | -52.4414 | |||
apbs-smol.in | 2-level focusing to 0.225 A, VdW surface, srfm smol | 1.3 | -54.0598 | -70.00 |
1.2.1 | -54.0598 | |||
1.2 | -54.05984 | |||
1.1.0 | -54.0587 | |||
1.0.0 | -54.0587 | |||
0.5.1 | -54.05873 | |||
0.5.0 | -54.70392 | |||
0.4.0 | -54.03931 | |||
0.3.2 | -57.1192 | |||
0.3.1 | -57.1192 | |||
0.3.0 | -57.1192 | |||
0.2.6 | -57.1192 | |||
0.2.5 | -57.1192 | |||
0.2.4 | -57.1192 | |||
0.2.3 | -57.1123 | |||
0.2.2 | -57.1123 | |||
0.2.1 | -57.112 | |||
0.2.0 | -57.711 | |||
0.1.8 | -58.51 |
1 The discrepancy in values between versions 0.4.0 and 0.3.2 is most likely due to three factors:
2 The discrepancy in values between versions 0.5.0 and 0.4.0 is most likely due to the following factor(s):
3 The discrepancy in values between versions 0.5.1 and 0.5.0 is most likely due to the following factor(s):
4 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. Please see the ChangeLog or the APBS documentation for more information.