I ran a molecular dynamics simulation for a system that consists of a peptide-protein complex, the binding happens at certain residues.
on calculating the MM-GBSA per residue energy decomposition using all the frames (1000 frame) I found that most of the residues participating in the binding have negative values.
only one residue in the peptide has a positive value however its binding residue has a negative value.
I double-checked the trajectory and the binding is stable during the course of the simulation.
is there an explanation for such a value, as I can not explain the reason behind it!
Hi Ahmed,
It looks really strange. Have you tried to use another frame interval of the trajectory to perform the calculation? Or have you used another end-point binding free energy method (e.g.: MM-PBSA)?
Kindly check the answers here
https://www.researchgate.net/post/Positive_binding_energy_from_MMPBSA_analysis
@Kauê Santana
I did the calculations for the whole trajectory, then I repeated it for the last 65 ns as it was the most stable in rmsd and the results were so close.
Also I did mmpbsa and the results was not far from what I got in mmgbsa.
@Jameel M. Abduljalil
I will try these solutions and update you, thanks Dr. Jameel
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