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I have used DOCK software to dock 10 ligands into the protein structure.

I want to generate a pdb file that contains all 10 binding modes of the ligands together with the protein. So all together in one pdb file.

Now, what I want to know is when I give this file to LIGPLOT, is it possible to generate something like:

%polar interactions XX %non-polar interactions XX %hydrogen interactions XX

Is there a way to do it with LIGPLOT, if now is there some other software that can be recommended for this type of assessment?

I have been having hard time, trying to find a way or software that can perform similar type of calculation and give me similar type of output that I want.

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  • $\begingroup$ "binding modes" --> "poses". You will need to do it programmatically. This post for example use Python pymol for querying atoms. Can you use Python, Perl or Julia? $\endgroup$
    – Matteo Ferla
    Apr 11, 2020 at 16:32
  • $\begingroup$ Yeah, I assumed so, cus it tends to be a bit more complicated. Unfortunately, I cant say for my self that I know any of the three languages :( $\endgroup$
    – djordje
    Apr 12, 2020 at 1:45

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You can visualize with Discovery Studio Visualizer and Schrodinger. Arpeggio and PLIP can generate output files of the different interactions.

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    $\begingroup$ Hey, thanks! already found that PLIP can do it and it works pretty well so I went for it. $\endgroup$
    – djordje
    Apr 24, 2020 at 10:51

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