Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein

Figure 6

(a) The initial structure of M2 TMD from the Protein Data Base (1NYJ). Trp-41 are shown in blue, His-37 in green, hydrophilic/charged amino acid side chains in light blue, all other side chains in yellow. (b) View along the channel with a network colored by the electrostatic potential (from blue to red corresponding to negative to positive). (c) Equilibrated box with a size of 60³ Ǻ³, containing 128 DMPC lipid, 3000 water molecules, and the M2 TMD structure in the centre.

(a)

(b)

(c)