# 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 File | Description | APBS Version | Results (kJ/mol) | UHBD (kJ/mol)
--- | --- | --- | --- | ---
apbs-mol.in | 2-level focusing to 0.225 A, VdW surface, srfm mol | 1.4.1-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:

- A bug fix in Vacc_molAcc which removed spurious regions of high internal dielectric values
- A switch in the algorithm used to compute the dielectric smoothing for srfm smol
- The addition of the Vacc sphere density (sdens keyword) as a variable and a change in the default sdens value from 3.0 to 10.0

2 The discrepancy in values between versions 0.5.0 and 0.4.0 is most likely due to the following factor(s):

- A change in the autofocusing routine for APBS

3 The discrepancy in values between versions 0.5.1 and 0.5.0 is most likely due to the following factor(s):

- Bug fix regarding multipole behavior for neutral proteins

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):

- Translation of contrib/pmgZ library from FORTRAN to C
- Differences in numerical implementations between FORTRAN and C compilers result in small round-off discrepencies
- Small margins due to these round-off discrepencies acumulate in the computations

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.