Actually if you have already calculated MM/GBSA for each frame (as far as I know, prime MM/GBSA needs separate .mae file for complex so it seems there is no obvious option to calculate using only Schrodinger) you could just calculate average in standard way and include this final step in your python script in any way you prefer. For example, like

from statistics import mean mean(MD_frames_mmgbsa)

Pousali Mitra

In Schrodinger, the MMGBSA calculation is calculated in two types: You can evaluate the overall free energy of the protein-ligand complex, and after MD simulation you can fragment the trajectories like each 10 frames (each 1 ns), 20 frames (2ns), and so on. Moreover, you can calculate the average if you need it.

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Waseem Ahmad Ansari,

Thank you for your answer. Yes, I need to do an average of the MM/GBSA for all trajectories. Can you please suggest me what should be the command for the average MM/GBSA calculation? Waseem Ahmad Ansari

Alisa Gorislav

Thank you for your reply.

Waseem Ahmad Ansari

I saw in your papers that you took 40-50 snapshots through the overall MD trajectories for MM/GBSA calculation. You used thrmal_mmgbsa.py script, but this script gave dG energy individually for each frame what you have taken 40-50 snapshots. Then how did you calculate the final dG energy for each complex? You did just simply average of each frame dG energy or something else? Can you please tell me how can you get the final binding free energies? It will be really helpful for me.