How do I add hydrogen atoms to my PDB file?

[Anonymous]

I’m currently using Rosetta 3.2.1, and I wish to add missing H atoms to my PDB file. I know that in the past, a clean_pdb.py script was created by the Meiler Lab to help with such a problem. However, I’m unable to locate this file anywhere in Rosetta 3.2.1. Is there any ways to locate this file or is there other scripts made to satisfy such a problem.?

Thanks.

[Anonymous]

I’ve forwarded this to one of the Meiler lab folks.

[Anonymous]

Is there a particular reason you need to pre-add hydrogens? As far as I’m aware, Rosetta will rebuild any missing atoms in input PDB files (including hydrogens) prior to using them.

If you’re looking for just the PDB with hydrogens attached, running them through the scoring application (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_score_commands.html) with the flags “-output” and “-no_optH false” should do the trick. (The latter option tells Rosetta to try to optimize polar hydrogen placement – put them in the best place for hydrogen bonding, etc.)

[Anonymous]

Oh okie, because I was looking through the rosetta tutorials, and I figured out that older PDB files might not have hydrogens attached, therefore it would be important to know how to add them. So does that mean, any Rosetta modules that I run will automatically add in the H atoms.?

[Anonymous]

You can find the script from the Meiler lab here:

http://www.meilerlab.org/index.php/jobs/resources

Rosetta adds the hydrogens for you. You simply need to pass the protein into any Rosetta protocol and the hydrogens will be placed.

[Anonymous]

By the way, Rosetta 3.2.1 doesn’t seem to have score.linuxgccrelease, it does have score_aln.linuxgccrelease and score_jd2.linuxgccrelease, and the flags looks much more complicated then score.linuxgccrelease. so how do I go abt doing it then.?

[Anonymous]

I’m not an expert on the scoring applications, but I think for simple uses, score_jd2 uses about the same flags as score. Certainly the input designation flags (“-in:file:s”, “-in:file:l” and “-in:file:silent”) and the “-output” and “-no_optH false” flags should be the same.

If you’re doing anything more complex, just do it how you normally would do it. That is, you don’t need to use two passes (one to add hydrogens and then a regular run) you can directly pass the hydrogen-free PDBs to enzyme design, or protein-protein docking or RosettaScripts, or whatever application, and Rosetta will take care of adding the hydrogens “under the hood”, so to speak.

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