Decomposition Analysis

[Raj Choudhary]

Hello Community

Can some body please explain me the reason behind the below given observation?

During decomposition analysis, on the command line it is showing a selection of 20 amino acids (for a distance within 5A) for my system. However, the results of the decomposition analysis is showing the interaction profile for only 9 out of the 20 amino acids initially selected.

Thank you in advance.

[Mario Sergio Valdes]

Do you mean the graphic or the output file?
To save space, amino acids with an energy contribution of less than (modular) 0.5 kcal/mol are not shown in the graphs. You can change both the cutoff value and whether or not to display them in the Init Dialog of gmx_MMPBSA_ana -> Decomposition Options/ Per-residue threshold and Decomposition Options/ Remove non-contributing residues, respectively.
Let me know if works for you

Mario S.

[Raj Choudhary]

Thank you for your prompt help. I was able to implement what you suggested.

Best regards

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