[Question]: Energy differences between WT and mutation

[WoutVanEynde]

Is it possible to use the software for the calculation of energy differences between a WT monomer and a mutated monomer, both of them are not a complex, so I cannot define a ligand and receptor. I have of both systems 100ns MD simulations.

[Valdes-Tresanco-MS]

Yes, you can.
Run both calculations and open them in the gmx_MMPBSA_ana app. Select which is the WT and the mutant in the configuration dialog. You will get the analysis charts for the WT, mutant and the delta

[WoutVanEynde]

Which groups should I select for receptor and ligand: complex and solvent? As it does not seem to be possible without the specification.

[Valdes-Tresanco-MS]

You should select according groups for both. For example, if you work with protein and ligand complexes, you must do 2 simulations, and select the 1 and 13 groups for both as a normal calculation. After the calculations are complete, open the gmx_MMPBSA_ana in the folder or define both with option -f path/to/folder-or-file. Then, in the configuration dialog, you can select which system you want to define as the wild type and the mutant as well.