README for pka-lig APBS examples

$Id: README.html 1600 2010-08-25 19:42:35Z yhuang01 $

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 1.3 8.0835 8.876
1.2.18.0835
1.28.08354
1.1.08.0858
1.0.08.0858
0.5.18.08583
0.5.08.0640
0.4.08.0640
apbs-smol-vdw.in 2-level focusing to 0.250 A spacing, VdW surface, srfm smol 1.3 20.9630 8.876
1.2.120.9630
1.220.96304
1.1.020.9628
1.0.020.9628
0.5.120.96283
0.5.020.9542
0.4.020.95422
0.3.28.06401
0.3.16.6465
0.3.06.6465
0.2.66.6465
0.2.56.6465
0.2.46.6465
0.2.36.6465
0.2.26.6465
0.2.16.647
0.2.06.647
0.1.86.65
apbs-mol-surf.in 2-level focusing to 0.250 A spacing, molecular surface, srfm mol 1.3 119.2608 86.50
1.2.1119.2608
1.2119.26084
1.1.0119.2607
1.0.0119.2607
0.5.1119.26073
0.5.0119.2347
0.4.0119.2347
apbs-smol-surf.in 2-level focusing to 0.250 A spacing, molecular surface, srfm smol 1.3 108.8748 86.50
1.2.1108.8748
1.2108.87484
1.1.0108.8773
1.0.0108.8773
0.5.1108.87733
0.5.0108.8540
0.4.0108.85402
0.3.294.87051
0.3.197.0147
0.3.097.0147
0.2.697.0147
0.2.597.0147
0.2.497.0147
0.2.397.0147
0.2.297.0147
0.2.197.015
0.2.097.015
0.1.897.01

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.