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 FileDescriptionAPBS VersionResults (kJ/mol)UHBD (kJ/mol)
apbs-mol.in 2-level focusing to 0.225 A, VdW surface, srfm mol 0.4.0-52.4414 -70.00
apbs-smol.in 2-level focusing to 0.225 A, VdW surface, srfm smol 0.4.0-54.03931 -70.00
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:

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