Musab Shahariar

>>First, Finish MD run → Ensure basename_water.sce (exists from your production MD)

>>Force field & box → Use the same FF as MD (default: AMBER14). PB requires a cuboid box; otherwise use BoundaryFast.

>>Receptor/ligand setup → Protein = object 1, ligand = object 2. If in same object, specify residues (ligres).

>>Edit macro (md_analyzebindenergy.mcr):

~Set MacroTarget '/path/to/basename'

~Set ForceField AMBER14

~Define snapshots to skip(remove equilibration)

~Set Solvation: BoundaryFast or PBS

~Docking: set as 'None', unless docking energies are required

>>Run macro → Options → Macro → Run → select md_analyzebindenergy.mcr.

>>Output → File basename_bindenergy (gives per-snapshot energies and average binding energy)

N.B: In YASARA, more positive = stronger binding.