[Question]: Unreasonable bond energy of ligand

[JiaqiBenWang]

My Question "Unreasonable bond energy of ligand"

Hi all. I am trying to calculate the binding energy of a protein homodimer (218 AA) and a peptide ligand (29 AA). However, the peptide ligand energy, especially the bond energy as well as its SD is much more higher (32x) than that of the receptor. Although the binding free energy is kind of okay (-47 kcal/mol, seems too high though), I am wondering what may cause this bizarre "bond energy of ligand" problem. I have run a 1500 ns MD simulations, and I used the frames from 500 ns to 1000 ns, with an interval of 2 ns. Relevant files are attached

40_MMPBSA.csv
40_MMPBSA.txt
mmpbsa.in.txt

Thanks much for your examination! More files can be found at (https://github.com/JiaqiBenWang/Unreasonable-bond-energy-of-ligand).

[Valdes-Tresanco-MS]

As you can see, the frame 33801 has a very high BOND/UB energy value.

This is probably related to the PBC, or the peptide is broken. Please, carefully check the structure.