[gmx-users] one protein and 4 ligands

[Mahboobeh Eslami]

Dear justinThank you so muchI did MD simulation on some protein-ligand complexes but I don't know that I must use one mol2 file for 4 ligands or  separate mol2 files for each ligand. I want to calculate free energy value for this complex by GMXPBSA script. Must free energy value be calculated for 4 lignads simultaneously? or I can calculate free energy value for each lignad individually.Thank you for kindness
Best wishes