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"
| Attachment | Size |
|---|---|
 Graft_FV_0001.txt | 9.78 KB |
Post Situation:
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.
I'd recommend using the "short protocol" as outlined in http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/dd/d... 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/d... 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.
Thank you very much for your reply. Using the short protocol worked just fine.