<p>So the 'right' answer here would be for you to use a <code>diff</code> tool of some kind (WinDiff, or just the diff command in a Unix-like environment). That would show you the exact added lines. (Although, trying this myself does not produce very clear results...)</p>
<p>However, I know from running <code>reduce</code> on PDB files that it's added a few things:</p>
<ul>
<li>The &quot;USER MOD&quot; lines, there's one on the first line and a large block just before the ATOM records</li>
<li>The hydrogen atoms, of course, needed for correct H-bond calculations</li>
</ul>
<p>As some commenters have pointed out, this should really be in the paper or other documentation for the tool.</p>

CC BY-SA 4.0
2023-01-10T12:45:55.980Z
2023-01-10T12:45:55.980Z
gilleain
<p>I used <a href="https://github.com/rlabduke/reduce" rel="nofollow noreferrer">a tool called reduce</a> to add Hydrogen bonds information to the PDB file.</p>
<p>I used the command:</p>
<pre><code>$ ./reduce -NOFLIP 2GB1.pdb &gt; 2GB1_with_H.pdb
</code></pre>
<p>The output file is supplied as follows:</p>
<ul>
<li><a href="https://textdoc.co/ZiuA0tY2elnoh5VK" rel="nofollow noreferrer">https://textdoc.co/ZiuA0tY2elnoh5VK</a></li>
</ul>
<p>I haven't understood the output.</p>
<p>What special change was made by the tool to the <code>2GB1.pdb</code> file?</p>

CC BY-SA 4.0
2023-01-09T21:27:50.037Z
Did you read [the paper](https://www.sciencedirect.com/science/article/abs/pii/S0022283698924019) and maybe contact the authors (http://kinemage.biochem.duke.edu/about/) if the paper doesn't make it clear?
Ram RS
CC BY-SA 4.0
2023-01-12T12:00:39.567Z
Are you sure its pdt format and not pdbqt ? (Didnt check , but never found it so far) :https://userguide.mdanalysis.org/1.1.1/formats/reference/pdbqt.html
pippo1980
<proteins><pdb>
What is changed in this PDB file?
# What is changed in this PDB file?

(Asked by: username_0 on 2023-01-09)

I used a tool called reduce to add Hydrogen bonds information to the PDB file.
I used the command:
$ ./reduce -NOFLIP 2GB1.pdb > 2GB1_with_H.pdb

The output file is supplied as follows:

https://textdoc.co/ZiuA0tY2elnoh5VK

I haven't understood the output.
What special change was made by the tool to the 2GB1.pdb file?

**Tags:** proteins, pdb
> **Comments:**
> **username_1**: Did you read [the paper](https://www.sciencedirect.com/science/article/abs/pii/S0022283698924019) and maybe contact the authors (http://kinemage.biochem.duke.edu/about/) if the paper doesn't make it clear?  
> **username_2**: Are you sure its pdt format and not pdbqt ? (Didnt check , but never found it so far) :https://userguide.mdanalysis.org/1.1.1/formats/reference/pdbqt.html  

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## 1 answers

### Answer by username_3 on 2023-01-10. Score: 6 | Accepted answer

So the 'right' answer here would be for you to use a `diff` tool of some kind (WinDiff, or just the diff command in a Unix-like environment). That would show you the exact added lines. (Although, trying this myself does not produce very clear results...)

However, I know from running `reduce` on PDB files that it's added a few things:

* The "USER MOD" lines, there's one on the first line and a large block just before the ATOM records
* The hydrogen atoms, of course, needed for correct H-bond calculations

As some commenters have pointed out, this should really be in the paper or other documentation for the tool.


---

