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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?

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    $\begingroup$ Does your ligand really have more than 300 atoms? $\endgroup$
    – Camps ♦
    Jun 6, 2020 at 17:03
  • $\begingroup$ no, infact I supposed that I made a mistake when i setup the system for MM-gbsa. When I have an output I open MM-GBSA panel and I select the prepared receptor and ligand from IFD output but dG output was upper than 50 million $\endgroup$
    – Giu
    Jun 6, 2020 at 17:20

1 Answer 1

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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).

enter image description here

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    $\begingroup$ +1. Maybe the user selected the receptor file where it should have been the ligand, leading to too many atoms. $\endgroup$
    – Nike Dattani
    Jun 6, 2020 at 19:26
  • $\begingroup$ Many thanks, i try to follow your advice but I have the same problem $\endgroup$
    – Giu
    Jun 7, 2020 at 10:53
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    $\begingroup$ Are you able to share your complex? $\endgroup$
    – Camps ♦
    Jun 7, 2020 at 13:45
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    $\begingroup$ I finally got it where I was wrong thanks your help. When I got the output from the induced fit docking I didn't split it into the receptor and ligand before doing the MM-GBSA. Thank you so much $\endgroup$
    – Giu
    Jun 10, 2020 at 18:05
  • $\begingroup$ Good to known everything is fine now. $\endgroup$
    – Camps ♦
    Jun 10, 2020 at 19:45

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