Five heavy-atom pair terms, all functions of the surface distance
d = r - R_i - R_j rather than the centre distance. The
rotatable-bond term divides rather than adds, penalising the entropy
a flexible ligand gives up on binding.
Usage
Vinasc(receptor, ligand_pose, n_rot = 0)
Arguments
- receptor
Matrix, rows [x, y, z, radius, type]; type 1
hydrophobic, 2 hydrogen-bond donor or acceptor, 0 otherwise.
- ligand_pose
Same layout for the ligand pose.
- n_rot
Active rotatable bonds between heavy atoms in the ligand.
Value
List with estimate, c_inter and the five
unweighted term sums.
References
Trott, O. & Olson, A. J. (2010). AutoDock Vina. Journal
of Computational Chemistry 31:455-461. Weights are table 1;
equation (9) is g(c_inter) = c_inter / (1 + w N_rot).
Examples
receptor <- cbind(c(0, 2, 4), c(0, 0, 0), c(0, 0, 0), c(1.9, 1.8, 1.9), c(1, 2, 0))
ligand <- cbind(c(0, 2), c(4, 4), c(0, 0), c(1.9, 1.8), c(1, 2))
Vinasc(receptor, ligand, n_rot = 2)$estimate
#> [1] -0.09303674
