README for hca-bind APBS examples

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 FileDescriptionAPBS VersionResults (kJ/mol)UHBD (kJ/mol)
apbs-mol.in 2-level focusing to 0.225 A, VdW surface, srfm mol 1.4.1-binary -52.46486 -70.00
1.4-51.46485
1.3-52.4647
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 1.4.1-binary -54.0598 -70.00
1.3-54.0598
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.

5 The discrepancy in values between versions 1.3 and 1.4 is most likely due to the following factor(s):

6 The discrepancy in the result between versions 1.4 and 1.4.1-binary is most likely due to a reporting error.

Please see the ChangeLog or the APBS documentation for more information.