apbs_electrostatics_README

Run PDB2PQR

• pdb2pqr --ff AMBER final_cg2at_de_novo_prot.pdb final_cg2at_de_novo_prot.pqr

Setup input for APBS and run

• vi final_cg2at_de_novo_prot.in
• apbs final_cg2at_de_novo_prot.in

Plot 2D map of APBS electrostatic surface along a certain Z dimension slice.

• conda activate base
• python apbs_2D_plot.py final_cg2at_de_novo_prot*.dx 90