. Author manuscript; available in PMC: 2014 Jul 25.

Published in final edited form as: J Chem Theory Comput. 2013 Jul 25;9(9):4046–4063. doi: 10.1021/ct4003702

Table 1.

The vdW parameters for protein backbone atoms.

Atom class	2r (Å)	ε (kcal/mol)	H-reduction factor
C_α	3.650	0.101
H_α	2.940	0.026	0.91
C_β	3.820	0.101
H_β	2.980	0.024	0.92
N (amide)	3.710	0.110
H (amide)	2.590	0.022	0.90
C (carbonyl)	3.820	0.106
O (carbonyl)	3.300	0.112
O^- (in −COO^-)	3.700	0.129
S	4.005	0.355
S^-	4.200	0.355

AMOEBA uses “atom classes” to define vdW and valence parameters while more finely-grained “atom types” are used for electrostatic parameters. Several different atom types may belong to the same atom class. r is the atomic radius; ε is the potential well depth; H-reduction factor accounts for the distance reduction that moves H vdW sphere off its nuclear center toward the heavy atom (X) it attaches to. The number represents the percentage of H-X bond length where the H atom vdW sphere is located at. Note that 2r (diameter) is used here to be consistent with TINKER parameter format.