I am confused why the ligand also showed in the decomposition analysis figure

[陳冠宇]

Dear Sir,

I defined two groups, one is the protein and the other is the ligand (F295) in my gmx_MMPBSA running job. 

  

After the decomposition analysis, I am confused why the ligand (F295 in my figure) also showed in the analysis figure (interaction residues analysis). I am not sure whether it is correct. Besides, I also noted that the energy of the ligand shown in the decomposition figure is not the same as shown in the enthalpy analysis figure. why?

I want to ask whether the results are correct or not. And, how to turn off the ligand shown in the figure after decomposition energy analysis. No matter what, It is used to analyze the interaction of each residue within some distance.

Looking forward to hearing from you soon.

Thank you very much.

Sincerely,

Mark

[Mario Sergio Valdes]

The energy decomposition consists of estimating the interaction energy either per-residue or per-wise. In the first case, the DELTA energy corresponds to the sum of the interaction energy of that residue with the rest of the selected residues and itself. In the second case, it is computed in pairs, i.e., the interaction energy between two residues. This is an approximation, which is not equivalent to the relative binding free energy value since it is computed only between the selected residues. The decomposition aims to estimate which residues are apparently more important for the interaction, useful when generating mutants (e.g. peptide design, in silico affinity maturation, etc.) In your case, the energy value reported for the ligand corresponds to the sum of the interaction energies between the ligand and the selected residues and itself. 

According to one of the figures, the interaction energy is approximately 40 kcal/mol. If you add up the interaction energy of all the residues shown in the decomposition plot, you get -41.28 kcal/mol, which is expected.
There is no way to remove the ligand from the graph in gmx_MMPBSA_ana, mainly because it would not be correct for the analysis. If your goal is to show only the receptor residues, edit the csv and use your favorite graphing program/library. If you have any doubts, I can help you set up the graph in the same format as shown in gmx_MMPBSA_ana.

To perform the decomposition analysis at least one residue of the ligand and the receptor is required, otherwise, there is no way to calculate the interaction energy, as the name suggests.

Let me know any doubt

Mario S.

[陳冠宇]

Dear Sir,

Thank you for responding so quickly. It is beneficial to me.

Sincerely,

Mark

***********************************

Mark, Guan-Yu Chen (陳冠宇) 

中國醫藥大學附設醫院 1JG1醫研部中醫藥研究發展中心

China Medicine Research and Development Center

China Medical University Hospital

Taiwan

Tel: +886-4-22053366 ext. 3316/5711

E-mail: markchen19822001(at)gmail.com 

E-mail: markchen19822001(at)yahoo.com.tw

祝 平安喜樂 ~ 福慧圓滿 ^^ 

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Mario Sergio Valdes <mariosergi...@gmail.com> 於 2022年11月30日 週三 晚上11:19寫道：

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