Hello everyone
I had a kinase+ATP-Mg complex. I ran MS simulation for 100 ns. via GROMACS and CHARMM36. The system is stable (backbone RMSD is and reach plateau before 20 ns.). When I used gmx_MMPBSA to calculate binding free energy (through decomposition to evaluate which residues are hotspots), I got standard deviation values for residues higher than the average energy. Any explanation/suggestion?
Your help is deeply appreciated.
Thnx.
At what time of the simulation was the binding free energy calculated?
Maybe the stability time frame is not selected.
I actually selected the last 50 ns of the trajectory (the most stable frames whose RMSDs and radii of gyration fluctuated within < 1 Å).
What is the resolution of your calculated binding energies? each frame?
Usually, MM-GBSA gives better results. Are you sure about the selection of the interacting molecules?
Abdo A Elfiky
Yes. The selection of groups for calculation was done properly (Protein and ATP).
The problem may be solved by choosing a time less than the end of the simulation. For example, calculate the binding free energy for the last 20 ns.
in GMX_MMPSA its recommended to use PB model with charmm force field. since you prepared your system using charmm36 you should calculate the binding free energy by MM-PBSA and set the PBRadii=7.
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