Journal for Biophysical Chemistry
Table 4 Summary of tuned IFF parameters (compared with the default values) required to bring adsorption free energies of the set of host–guest peptides into agreement with experiment for the silica glass surface
Residue | Atom type (IUPAC name) | LJ (ε) | Partial charge | ||
|---|---|---|---|---|---|
CHARMM | Tuned | CHARMM | Tuned | ||
TIP3P | OT | −0.1521 | −0.2053 | −0.834 | −0.950 |
HT | −0.0460 | −0.0621 | 0.417 | 0.475 | |
Trp | CY (CG) | −0.0700 | −0.0350 | −0.030 | −0.030 |
CA (CD1, CE3, CZ3, CZ2, CH2) | −0.0700 | −0.0350 | −0.115 | −0.115 | |
HP (HD1, HE3, HZ3, HZ2, HH2) | −0.0300 | −0.0150 | 0.115 | 0.115 | |
NY (NE1) | −0.2000 | −0.1000 | −0.610 | −0.610 | |
H (HE1) | −0.0460 | −0.0230 | 0.380 | 0.380 | |
CPT (CD2) | −0.0900 | −0.0450 | −0.020 | −0.020 | |
CPT (CE2) | −0.0900 | −0.0450 | 0.130 | 0.130 | |
Silica | Si | −0.3000 | −0.1800 | 0.900 | 0.900 |
O | −0.1500 | −0.0900 | −0.450 | −0.450 | |
O (H) | −0.1521 | −0.0913 | −0.660 | −0.660 | |
H | −0.0460 | −0.0276 | 0.430 | 0.430 | |