Hi,

just add the following lines (also to AD4.1_bound.dat):

atom_par Na 3.98 0.030 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Sodium

atom_par As 4.23 0.309 13.000 -0.00110 0.0 0.0 0 -1 -1 1 # Arsenic

The AD4_parameters.dat file is a parameter file used by the AutoDock4 software for molecular docking simulations. To add Sodium and Arsenic atoms to this parameter file, you will need to modify the file by adding the parameters for these atoms.

Here are the steps you can follow to add Sodium and Arsenic atoms to the AD4_parameters.dat file:

The first line defines the parameters for Sodium, and the second line defines the parameters for Arsenic. Each line contains the following information:

• Atom symbol (Na or As)
• Atomic number (11 for Sodium, 33 for Arsenic)
• Atomic mass (22.98977 for Sodium, 74.92160 for Arsenic)
• Charge (0.0 for both Sodium and Arsenic)
• Van der Waals radius (1.55 Å for Sodium, 2.08 Å for Arsenic)
• Electronegativity (0.0 for both Sodium and Arsenic)
• Polarizability (0.0 for both Sodium and Arsenic)
• Surface tension (0.0 for both Sodium and Arsenic)

Once you have added the parameters for Sodium and Arsenic, you can use these atoms in your molecular docking simulations with AutoDock4. Note that you may also need to modify other files, such as the ligand and receptor input files, to include Sodium and Arsenic atoms in your system.