APBS examples/test cases

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



Results

Actin-Dimer

  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

  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

-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

  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

  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

  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

  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

  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

  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