Table 4.
RMSDs between the MM and QM 2D potential energy surfaces for the χ1 and χ2 torsions in amino acid (X) dipeptides capped with N-acetyl and N’-methylamide moieties using the Drude-2013 and Drude-2019 FFs. RMSD with all conformations (RMSD-ALL) and with the conformations excluding the energy cutoff (kcal/mol) regions (w/Cutoff) are shown. The RMSDs from the initial fitting results are shown in the Initial w/Cutoff column, and from the final results of Drude-2019 FF are shown in the Final w/Cutoff.
| Dipeptides | Drude-2013 | Drude-2019 | |||||
|---|---|---|---|---|---|---|---|
| X | Cutoff | RMSD-ALL | w/Cutoff | RMSD-ALL | w/Cutoff | Initial w/Cutoff | Final w/Cutoff |
| ARG | 20 | 4.57 | 4.35 | 2.43 | 2.38 | 1.95 | 2.38 |
| ASN | 12 | 2.62 | 2.61 | 1.75 | 1.63 | 1.63 | 1.63 |
| ASP | 25 | 3.50 | 2.94 | 3.57 | 3.09 | 1.83 | 3.09 |
| CYS | 12 | 1.31 | 1.28 | 1.15 | 1.10 | 1.10 | 1.10 |
| GLN | 12 | 2.65 | 2.39 | 1.97 | 1.54 | 1.46 | 1.54 |
| GLU | 25 | 8.23 | 8.25 | 4.00 | 3.86 | 2.40 | 3.86 |
| HSD | 12 | 1.70 | 1.51 | 1.40 | 1.23 | 1.22 | 1.23 |
| HSE | 12 | 2.16 | 1.99 | 1.42 | 1.32 | 1.29 | 1.32 |
| HSP | 25 | 2.16 | 2.15 | 1.60 | 1.59 | 1.59 | 1.59 |
| ILE | 12 | 2.58 | 2.21 | 2.54 | 2.31 | 1.46 | 2.31 |
| LEU | 12 | 2.07 | 1.72 | 1.74 | 1.43 | 1.22 | 1.43 |
| LYS | 20 | 5.27 | 4.95 | 2.44 | 2.49 | 1.80 | 2.49 |
| MET | 12 | 2.43 | 2.30 | 1.89 | 1.49 | 1.39 | 1.49 |
| PHE | 12 | 1.41 | 1.25 | 1.11 | 1.04 | 1.04 | 1.04 |
| SER | 12 | 1.38 | 1.36 | 2.32 | 2.32 | 1.04 | 2.32 |
| THR | 12 | 1.86 | 1.72 | 2.14 | 2.18 | 1.28 | 2.46 |
| TRP | 12 | 1.78 | 1.63 | 1.50 | 1.29 | 1.13 | 1.29 |
| TYR | 12 | 1.55 | 1.31 | 1.33 | 1.06 | 1.06 | 1.06 |
| VAL | 12 | 1.24 | 1.18 | 1.38 | 1.32 | 1.20 | 1.32 |
| Average | 2.66±0.40 | 2.48±0.40 | 1.98±0.19 | 1.82±0.17 | 1.43±0.08 | 1.84±0.18 | |
Errors represent standard errors over the amino acids.