How can an MM-GBSA(molecular mechanics energies combined with generalized Born and surface area continuum solvation) calculation be done from an induced fit docking (IFD) output? I performed an IFD and now I would like to run an MM-GBSA calculation, but when I try to start it, I get a warning message that says: The ligand contains more than 300 atoms and the output is very big. Could you please explain what I have to do for performing this calculation?
The Prime MM-GBSA panel is bellow.
As you can see, the first section is about choosing the structures to calculate the MM-GBSA energy.
The marked option works only for pose viewer files. IFD don't create this kind of file. If you want to use it, you need to work with some scripts/export in order to convert a mae (or maegz) file into a .pv.mae (or .pv.maegz) file and then use this option.
The second option is to separate the complex into two structure files: one for the protein and one for the ligand. Again, you can do this using the table or using the scripts. Here you have to be careful to not exchange the files (selecting the receptor file in the ligand selection will give you an error about the number of atoms).