Rosetta 3.4 “Relax pdb with allatom constraints” does not work with structures containing multiple chains

[Anonymous]

I am trying to use “Relax pdb with allatom constraints” to prepare starting files. This works fine as long as the input pdb contains only a single chain. If it contains two chains, relaxation fails (see attached log file). Although each of the component chains runs fine on its own, as soon as I try to process the complex, the process fails with a complaint about missing atoms:
“[ERROR] Exception caught by JobDistributor for job Graft_FV_0001_0001Atom CG 122 not found”

[Anonymous]

Does your constraint file use PDB numbering, or Rosetta numbering-from-one? The error “Atom CG 122” not found sounds to me like your constraint file specifies an atom that isn’t there.

[Anonymous]

I’d recommend using the “short protocol” as outlined in http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/dd/da1/preparing_structures.html it’s more-or-less equivalent to the longer protocol and much easier. (Not mentioning it in the “Prepare PDB for Rosetta with Relax” page http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d9/d2e/prepare_pdb_for_rosetta_with_relax.html is a regrettable oversight.)

While sidechain_cst_3.py attempts to match the internal Rosetta numbering scheme when generating constraints, it doesn’t always get things right. By doing the constraint generation within Rosetta itself, it’s easier to get right.

[Anonymous]

Thank you very much for your reply. Using the short protocol worked just fine.

[Author]

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