Figure 7. The setup of the molecular dynamics simulation of Cav1.2 channel in pure POPC.

(1) Generate the topology file of LCC model conformation from homology modeling. (2) For POPC environment, replicate the starting configuration of a 128-lipid POPC bilayer in X and Y axis to create of a bilayer of 512 lipids. (3) Superimpose the LCC model with POPC and POPC/CHOL bilayer. (4) Compress and locate the channel in the center of bilayer and minimize the whole system. (5) Insert the 5 Ca²⁺ along the pore of LCC model. (6) Solvate water TIP3P, add NaCl neutralize system by adding Na⁺ ion.