Table 4 Optimal scaling factors for the MM/GBSA model and the MM/GBSA(+HB) model: analysis of the λ repressor-operator system (λ), of the Cro-operator system (Cro) and the joint analysis (λ + Cro). Standard deviations (see Methods section) are given in parentheses.
MM/GBSA | λ | Cro | λ + Cro |
|---|---|---|---|
x Coul | 0.157 (0.045) | 0.132 (0.067) | 0.153 (0.037) |
x vdW | 0.252 (0.124) | 0.332 (0.132) | 0.313 (0.086) |
x GB | 0.142 (0.046) | 0.121 (0.069) | 0.145 (0.038) |
x P | -0.010 (0.012) | 0.019 (0.012) | -0.009 (0.006) |
x H | -0.029 (0.008) | -0.009 (0.011) | -0.031 (0.005) |
x const | -11.744 (28.025) | 70.791 (37.615) | -19.519(11.903) |
MM/GBSA(+HB) | λ | Cro | λ + Cro |
x Coul | 0.042 (0.053) | 0.016 (0.066) | 0.051 (0.041) |
x vdW | 0.206 (0.113) | 0.219 (0.118) | 0.262 (0.079) |
x GB | 0.025 (0.054) | 0.002 (0.068) | 0.043 (0.041) |
x P | -0.016 (0.011) | -0.001 (0.012) | -0.024 (0.006) |
x H | -0.023 (0.008) | -0.005 (0.010) | -0.029 (0.005) |
x HB | -0.533 (0.156) | -0.879 (0.224) | -0.561 (0.125) |
x const | 13.699 (26.308) | 65.011 (32.867) | -21.595 (10.908) |