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 | 1.2.1 | 8.0835 | 8.876 |
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 | 1.2.1 | 20.9630 | 8.876 |
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 | 1.2.1 | 119.2608 | 86.50 |
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 | 1.2.1 | 108.8748 | 86.50 |
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:
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.