# README for pka-lig APBS examples

The example input files in this directory calculate the binding energes of a ligand to protein kinase A.

This example was contributed by Chung Wong.

Input File | Description | APBS Version | Results (kJ/mol) | UHBD (kJ/mol)
--- | --- | --- | --- | ---
apbs-mol-vdw.in | 2-level focusing to 0.250 A spacing, VdW surface, srfm mol | 1.4.1-binary | 8.0835 | 8.876
1.4 | 8.0835
1.3 | 8.0835
1.2.1 | 8.0835
1.2 | 8.08354
1.1.0 | 8.0858
1.0.0 | 8.0858
0.5.1 | 8.08583
0.5.0 | 8.0640
0.4.0 | 8.0640
apbs-smol-vdw.in | 2-level focusing to 0.250 A spacing, VdW surface, srfm smol | 1.4.1-binary | 20.9630 | 8.876
1.4 | 20.9630
1.3 | 20.9630
1.2.1 | 20.9630
1.2 | 20.96304
1.1.0 | 20.9628
1.0.0 | 20.9628
0.5.1 | 20.96283
0.5.0 | 20.9542
0.4.0 | 20.95422
0.3.2 | 8.06401
0.3.1 | 6.6465
0.3.0 | 6.6465
0.2.6 | 6.6465
0.2.5 | 6.6465
0.2.4 | 6.6465
0.2.3 | 6.6465
0.2.2 | 6.6465
0.2.1 | 6.647
0.2.0 | 6.647
0.1.8 | 6.65
apbs-mol-surf.in | 2-level focusing to 0.250 A spacing, molecular surface, srfm mol | 1.4.1-binary | 119.2608 | 86.50
1.4 | 119.2608
1.3 | 119.2608
1.2.1 | 119.2608
1.2 | 119.26084
1.1.0 | 119.2607
1.0.0 | 119.2607
0.5.1 | 119.26073
0.5.0 | 119.2347
0.4.0 | 119.2347
apbs-smol-surf.in | 2-level focusing to 0.250 A spacing, molecular surface, srfm smol | 1.4.1-binary | 108.8773 | 86.50
1.4 | 108.87735
1.3 | 108.8748
1.2.1 | 108.8748
1.2 | 108.87484
1.1.0 | 108.8773
1.0.0 | 108.8773
0.5.1 | 108.87733
0.5.0 | 108.8540
0.4.0 | 108.85402
0.3.2 | 94.87051
0.3.1 | 97.0147
0.3.0 | 97.0147
0.2.6 | 97.0147
0.2.5 | 97.0147
0.2.4 | 97.0147
0.2.3 | 97.0147
0.2.2 | 97.0147
0.2.1 | 97.015
0.2.0 | 97.015
0.1.8 | 97.01

1 The grid dimensions (dime) changed from 65^3 to 97^3 in the 0.3.2 release to give a finer mesh.

2 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

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

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