Reply To: How do I add hydrogen atoms to my PDB file?

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March 31, 2011 at 4:20 pm #5273
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.