Let us say binding free energy is -80, then + 130 kJ/mol error bar.
So how far is it correct?
Your system is not well equilibrated, how many frames did you used to calculate this binding free energy?
Plus, MM/PBSA is more like qualitative method than quantitative. TO get a better results, you need to focus on the trajectory where the RMSD fluctuations are minimal. Moreover, you can trim/exclude the initial frames where the structure is undergoing higher fluctuation, it can also improve the result.
Thank you, Ayaz Anwar and I took 1k frames out of 20ns trajectory (skipped the frames accordingly).
why method did you use? 1-trajectory or 3-trajectory? In 3-trajectory protocol, the standard deviation of energy is pretty high because the internal energy component
You need to run longer simulation to get any meaningful results as 20ns is not sufficient. At least 100ns * 3 replicates can provide you reasonable results.
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