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) |
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) |
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 | -11.975|
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 |
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 |
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 |
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 |
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 |
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 |
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 |