Dear Amber users,
I am trying to calculate binding free energy using *MMPBSA.py* for a
protein–protein system after running standard MD simulations. The MD part
completed successfully without any issues.
For the MMPBSA calculation, I generated the necessary parameter/topology
files (protein-ligand.prmtop, protein.prmtop, and ligand.prmtop). However,
when I run the MMPBSA job, it fails with the following error:
CalcError: /home/Software/amber16/bin/mmpbsa_py_energy failed with
prmtop protein-ligand.prmtop!
PB Bomb in pb_aaradi(): No radius assigned for atom 6513 OG OZ
It seems that the PB calculation cannot assign a radius to this atom type
(OG/OZ). I did not face this issue during normal MD runs — it only appears
during MMPBSA.
Could someone please suggest what might be causing this issue and how to
fix it?
-
Do I need to adjust radii parameters for non-standard residues (e.g.,
phosphorylated residues like SEP)?
-
Or should I regenerate the prmtop files with specific options to avoid
this problem?
Any guidance would be greatly appreciated.
Best regards,
Angad Sharma
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Received on Wed Sep 24 2025 - 06:00:03 PDT
