I have run a 30ns simulation for my receptor-ligand complex. I would like to know how much of the output I should use for an MM-PBSA analysis (For example, in some publications, only the last 10ns are used or only a number of frames taken at particular intervals are used).
Hello M.Sc. Mayur Mukhi
Indeed, you can find in the literature that there are different times taken from the last MD simulations to calculate binding free energy with MM-PBSA (for example, for 10 to 50 ns).
But I guess is better to average the results predicted using several independent MD trajectories. For example, you can use a short production (always take care of that your system is well equilibrated) but with 50 independent MD running. There are a lot of literature that support this. You would like to read the review:
Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z., & Hou, T. (2019). End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design. Chemical reviews, 119(16), 9478-9508.
Dear Mayur
firstly analyse the RMSD plot of protein ligand complex and see when they become stable. Once the complex is stable, its good to take more number of poses for analysis. More the number of poses more is the prediction accuracy.
So, it all depend on your total MD run time frame. Generally speaking anything which is more than 15 to 20 ns stable at a particular time frame you can use the poses for analysis.
regards
Tanuj
Mayur Mukhi Edward Francisco Méndez Otálvaro Tanuj Sharma check our new tool, gmx_MMPBSA... there you can check for stability of the calculated energy and have a better idea of which interval to chose
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/analyzer/#types-of-charts
gmx_MMPBSA is compatible with all GROMACS... Different calculations can be performed with this tool, including but not limited to:
-binding free energy calculations with different implicit solvent model (PB, GB, and RISM)
-alanine scanning
-energy decomposition
-entropy corrections
-QM/MMGBSA
check this summary in the documentation for more details
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/getting-started/
don't hesitate to contact us if you need any help
best!
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