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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:

I haven't understood the output.

What special change was made by the tool to the 2GB1.pdb file?

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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.

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