README for FKBP APBS examples


The example input files in this directory simulate the binding of various (small) ligands to FKBP. Analogous to HCA binding case (except it works).

In order to calculate solvation energy upon binding you will need to take the results from these input files and subtract from them the results obtained from the coulomb utility found at apbs/tools/manip/coulomb. The values returned from this utility are:

This example was contributed by Jung-Hsin Lin.

Input FileDescriptionAPBS VersionResults (kJ/mol)UHBD (kJ/mol)
1d7h-dmso/apbs-mol.in 1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm mol 0.4.015.0089 19.097
1d7h-dmso/apbs-smol.in 1d7h-dmso, 2-level focusing to 0.225 A, VdW surface, srfm smol 0.4.016.24581 19.097
0.3.215.0089
0.3.115.0089
0.3.015.0089
0.2.615.0089
0.2.515.0089
0.2.415.0089
0.2.315.0097
0.2.214.5886
0.2.114.589
0.2.014.589
0.1.814.591
1d7i-dss/apbs-mol.in 1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm mol 0.4.014.4254 16.231
1d7i-dss/apbs-smol.in 1d7i-dss, 2-level focusing to 0.225 A, VdW surface, srfm smol 0.4.015.45171 16.231
0.3.214.4254
0.3.114.4254
0.3.014.4254
0.2.614.4254
0.2.514.4254
0.2.414.4254
0.2.314.4254
0.2.214.3865
0.2.114.387
0.2.014.387
0.1.815.210

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.