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    As far as the energy function: poke around the other topics and you’ll find it’s reasonably well covered already (or at least, any answers that aren’t linked to here aren’t written down.) Read the Rohl 2004 MIE review paper and Kuhlman’s top7 paper supplemental, plus look at the Meiler lab documentation (rosetta tab).

    As far as hydrogens: Rosetta adds them automatically. For total scores of positive hundreds, there are significant clashes in the structures anyway, so it hardly matters how hydrogens are added. For some structures, you may see some score difference using hydrogens from an external program; assuming their PDB atom names are correct (this is not the common state, sadly) Rosetta will read them in and use them. Use the -no_optH flag for this.