README for pka-lig APBS examples

$Id: README.html 1264 2008-04-16 16:41:31Z 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 1.0.0 8.0858 8.876
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 1.0.0 20.9628 8.876
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 1.0.0 119.2607 86.50
0.5.1119.26073
0.5.0119.2347
0.4.0119.2347
apbs-smol-mol.in 2-level focusing to 0.250 A spacing, molecular surface, srfm smol 1.0.0 108.8773 86.50
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):

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