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

CC BY-SA 4.0
2020-04-24T10:51:17.463Z
Hey, thanks! already found that PLIP can do it and it works pretty well so I went for it.
djordje
CC BY-SA 4.0
2020-04-24T08:25:23.957Z
2020-04-24T08:25:23.957Z
BND
<p>I have used DOCK software to dock 10 ligands into the protein structure.</p>

<p>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.</p>

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

<p>%polar interactions XX
%non-polar interactions XX
%hydrogen interactions XX</p>

<p>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?</p>

<p>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.</p>

<p>Best</p>

CC BY-SA 4.0
2020-04-11T16:32:03.453Z
"binding modes" --> "poses".

You will need to do it programmatically. [This post for example use Python pymol](https://bioinformatics.stackexchange.com/questions/12862/extract-autodocked-protein-ligand-connections-programatically/12888#12888) for querying atoms. Can you use Python, Perl or Julia?
Matteo Ferla
CC BY-SA 4.0
2020-04-12T01:45:38.187Z
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 :(
djordje
<proteins><protein-structure><docking>
Visualizing protein-ligand interactions with LIGPLOT or any other suitable software?
# Visualizing protein-ligand interactions with LIGPLOT or any other suitable software?

(Asked by: username_0 on 2020-04-11)

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.

Best

**Tags:** proteins, protein-structure, docking
> **Comments:**
> **username_1**: "binding modes" --> "poses".  You will need to do it programmatically. [This post for example use Python pymol](https://bioinformatics.stackexchange.com/questions/12862/extract-autodocked-protein-ligand-connections-programatically/12888#12888) for querying atoms. Can you use Python, Perl or Julia?  
> **username_0**: 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 :(  

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## 1 answers

### Answer by username_2 on 2020-04-24. Score: 1 | Accepted answer

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

> **Comments:**
> **username_0**: Hey, thanks! already found that PLIP can do it and it works pretty well so I went for it.  

---

