APBS examples/test cases

$Id: README.html,v 1.18 2004/01/20 16:49:18 apbs Exp $

Results

Actin-Dimer

Source: Dave Sept
Description: Calculate binding energies for actin dimers. This is an example of a large biomolecule binding energy calculation that often requires parallel focusing.

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
Parallel, 8 proc, ~0.9 A spacing, LPBE	91.67	91.939	91.945	91.9450	90.2543	90.2573	90.2573	90.2573	90.2573	106.7 (1.00 A res., NPBE)
Sequential, 2-level focus to <=0.725 A, NPBE	90.84	90.829	90.829	90.829	88.6064	88.6101	88.6101	88.6101	88.6101	106.7 (1.00 A res., NPBE)

Born Ion

Source: Nathan Baker
Description: Calculate solvation energies for ions of various sizes and compare to the analytical results.

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
3 A sphere, 3-level focus to 0.188 A, srfm 0, chgm 0	-229.72	-229.72	-229.72	-229.725	-229.7250	-229.7250	-229.7250	-229.7250	-229.7250	-228.57 kJ/mol (3 A sphere)
3 A sphere, 3-level focus to 0.188 A, srfm 0, chgm 1	-227.19	-227.19	-227.19	-227.186	-227.1859	-227.1859	-229.7248	-229.7248	-229.7248	-228.57 kJ/mol (3 A sphere)
3 A sphere, 4-proc 3-level para focus to 0.103 A, srfm 1, chgm 1	-226.23	-226.228	-230.77 (srfm 0)	-226.2276	-226.2276	-226.2276	-229.5849	-229.5849	-229.5849	-228.57 kJ/mol (3 A sphere)

FKBP

Source: Jung-Hsin Lin
Description: Binding of various (small) ligands to FKBP. Analogous to HCA binding case (except it works).

-11.975

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
1D7H-DMSO - 2-level focusing to 0.225 A, VdW surface, DGbind(solv)	18.591	14.589	14.589	14.5886	15.0097	15.0089	15.0089	15.0089	15.0089	19.097
1D7H-DMSO - 2-level focusing to 0.225 A, VdW surface, DGbind(Coul)	-15.103	-15.103	-15.093	-15.0930	-15.0930	-15.0930	-15.0930	-15.0930	-15.0930	-15.103
1D7H-DMSO - 2-level focusing to 0.225 A, VdW surface, DGbind	3.448	-0.514	-0.504	-0.5043	-0.0833	-0.0841	-0.0841	-0.0841	-0.0841	3.994
1D7I-DSS - 2-level focusing to 0.225 A, VdW surface, DGbind(solv)	15.210	14.387	14.387	14.3865	14.4261	14.4254	14.4254	14.4254	14.4254	16.231
1D7I-DSS - 2-level focusing to 0.225 A, VdW surface, DGbind(Coul)	-11.975	-11.975	-11.967	-11.9670	-11.9670	-11.9670	-11.9670	-11.9670	-11.9670
1D7I-DSS - 2-level focusing to 0.225 A, VdW surface, DGbind	3.235	2.412	2.420	2.4195	2.4591	2.4585	2.4585	2.4585	2.4585	4.256

hca-bind

Source: UHBD
Description: Calculate the binding of a small molecule (acetazolamide) to a medium-sized protein (human carbonic anhydrase).

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
2-level focus to 0.225 A, srfm 1, VdW surf, Directly-calculated Binding Energy	-58.51	-57.711	-57.112	-57.1123	-57.1123	-57.1192	-57.1192	-57.1192	-57.1192	-70.00

ionize

Source: UHBD
Description: Calculate electrostatic contributions to the ionization energy of acetic acid.

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
3-level focusing to 0.094 A, Acetic acid solv. G	-22.63	-22.627	-22.627	-22.628	-22.629	-22.6787	-22.6787	-22.6787	-22.6787	-22.22
3-level focusing to 0.094 A, Acetate solv. G	-195.31	-195.305	-195.305	-195.3051	-195.3135	-199.7462	-199.7462	-199.7462	-199.7462	-198.04
3-level focusing to 0.094 A, Proton solv. G	290.86	-290.859	-290.859	-290.8591	-290.8751	-297.4599	-297.4599	-297.4599	-297.4599	-295.79
3-level focusing to 0.094 A, Ionization Energy	-463.54	-463.537	-463.537	-463.5373	-463.5617	-474.5273	-474.5273	-474.5273	-474.5273	-471.61

ion-protein

Source: Dave Sept
Description: Calculate energy of placing an ion near a macromolecule

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
0.53 A resolution, NPBE, prot. diel. of 12	18.90	18.895	18.895	18.8953	17.4049	17.4207	17.4207	17.4207	17.4207	18.39
0.53 A resolution, NPBE, prot. diel. of 2	21.45	21.453	21.453	21.4530	19.8652	19.8794	19.8794	19.8794	19.8794	23.58

pka-lig

Source: Chung Wong
Description: Calculate binding energies of a ligand to protein kinase A.

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
2-level focusing to 0.250 A spacing, vdw-based dielectric	6.65	6.647	6.647	6.6465	6.6465	6.6465	6.6465	6.6465	6.6465	8.876
2-level focusing to 0.250 A spacing, mol surf-based dielectric	97.01	97.015	97.015	97.0147	97.0147	97.0147	97.0147	97.0147	97.0147	86.50

point-pmf

Source: Nathan Baker
Description: See how well we do reproducing Coulomb's law.

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
1 A dist	18.308	18.31	18.308	18.3082	18.3082	18.3082	18.3082	18.3082	18.3082	17.686
2 A dist	8.907	8.91	8.907	8.9067	8.9067	8.9067	8.9067	8.9067	8.9067	8.843
3 A dist	5.910	5.91	5.910	5.9096	5.9096	5.9096	5.9096	5.9096	5.9096	5.89533
4 A dist	4.430	4.43	4.430	4.4301	4.4301	4.4301	4.4301	4.4301	4.4301	4.4215

solv

Source: UHBD
Description: Calculate the solvation energies of methanol and methoxide.

	APBS Version - Results in kJ/mol
Example	0.1.8	0.2.0	0.2.1	0.2.2	0.2.3	0.2.4	0.2.5	0.2.6	0.3.0	UHBD/Analytical
Methanol, 0.250 A spacing, zero probe radius, srfm 1	-36.222	-36.222	-36.222	-36.2223	-36.2223	-36.2486	-36.6249	-36.6249	-36.6249	-35.595
Methoxide, 0.250 A spacing, zero probe radius, srfm 1	-391.800	-391.800	-391.800	-391.7995	-391.7995	-390.4119	-390.4119	-390.4119	-390.4119	-390.023
Difference	-355.577	-355.577	-355.577	-355.5772	-355.5771	-354.1632	-354.1632	-354.1632	-354.1632	-354.424