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
&general
endframe=50, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
Many thanks for any ideas in advance