Table 1.
Final atomic input radii for the optimized GBMV2 implicit solvent protein force field. The default CHARMM36 vdW radii are used for all atoms not shown.
| Group | Atom | vdW (Å) | GBMV2 (Å) |
|---|---|---|---|
| Hydrogen | Varies | – | |
| Backbone | O | 1.70 | 1.65 |
| N | 1.85 | 1.77 | |
| C | 2.06 | 2.05 | |
| CA | 2.06 | – | |
| Sidechains | |||
| All | CB | 2.175 | – |
| CD, CG | 2.275 | – | |
| Lys | NZ | 1.85 | – |
| CE | 2.175 | 2.14 | |
| Arg | NH* | 1.85 | 1.88 |
| NE | 1.85 | 1.95 | |
| CZ | 2.00 | 2.06 | |
| Glu | OE* | 1.70 | 1.68 |
| CD | 2.00 | 2.10 | |
| Gln | NE2 | 1.85 | 1.91 |
| OE*, OD* | 1.70 | – | |
| Hsp | ND1, NE2 | 1.85 | 1.82 |
| His/Hsd | ND1 | 1.85 | 1.82 |
| NE2 | 1.85 | 1.80 | |
*
is a wildcard character.
–
denotes no change from the default CHARMM36 vdW radius.