Running gmx_MMPBSA for gromacs files

Dear Gromacs users,

I am trying to calculate binding free energy between protein and ligand using gmx_MMPBSA package. My trajectory and topology file (stripped of water and ions) were created successfully, however when running gmx_MMPBSA I get the following error:

"PrmtopError: provided receptor/ligand masks don’t select every atom in the complex topology!

Exiting. All files have been retained."

I will post my mmpbsa input script below if that helps:

Input file for running PB and GB in serial


endframe=50, keep_files=2,



igb=2, saltcon=0.100,





Many thanks for any ideas in advance

gmx_MMPBSA is not part of the Gromacs tools package. Please consult our group ( directly or open an issue on Github (Issues · Valdes-Tresanco-MS/gmx_MMPBSA · GitHub) for proper follow-up
Mario S.