Table 1. Polypeptides Used in Simulations.
| no. | sequence | ionization degree | force field |
|---|---|---|---|
| 1 | ACE-(Glu–)15-NME | 1 | AMBER99SB*-ILDNP |
| 2 | CHARMM27 | ||
| 3 | OPLS-AA | ||
| 4 | ACE-Glu–-Glu-(Glu–)2-Glu-(Glu–)2-Glu-(Glu–)2-Glu-(Glu–)2-Glu-Glu–-NME | 0.66 | AMBER99SB*-ILDNP |
| 5 | CHARMM27 | ||
| 6 | OPLS-AA | ||
| 7 | ACE-Glu-Glu–-(Glu)2-Glu–-(Glu)2-Glu–-(Glu)2- Glu–-(Glu)2-Glu–-Glu-NME | 0.33 | AMBER99SB*-ILDNP |
| 8 | CHARMM27 | ||
| 9 | OPLS-AA | ||
| 10 | ACE-(Glu)15-NME | 0 | AMBER99SB*-ILDNP |
| 11 | CHARMM27 | ||
| 12 | OPLS-AA | ||
| 13 | ACE-(Lys+)15-NME | 1 | AMBER99SB*-ILDNP |
| 14 | CHARMM27 | ||
| 15 | OPLS-AA | ||
| 16 | ACE-Lys+-Lys-(Lys+)2-Lys-(Lys+)2-Lys-(Lys+)2-Lys-(Lys+)2-Lys-Lys+-NME | 0.66 | AMBER99SB*-ILDNP |
| 17 | CHARMM27 | ||
| 18 | OPLS-AA | ||
| 19 | ACE-Lys-Lys+-(Lys)2-Lys+-(Lys)2-Lys+-(Lys)2-Lys+-(Lys)2-Lys+-Lys-NME | 0.33 | AMBER99SB*-ILDNP |
| 20 | CHARMM27 | ||
| 21 | OPLS-AA | ||
| 22 | ACE-(Lys)15-NME | 0 | AMBER99SB*-ILDNP |
| 23 | CHARMM27 | ||
| 24 | OPLS-AA |