[gmx-users] one protein and 4 ligands

[Mahboobeh Eslami]

I want to do MD simulation on a protein-ligand complex. the protein includes 4 chains and the ligands are ASP amino acid. I want to use Amber topologies from acpype for generating necessary files for ligands. please guide me to do this work correctly.  Can I use GMXPBSA script to obtain free energy value for the studied protein-ligand complex.Thank you so muchBest wishes