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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"

I'm wondering whether there is improvement of model generation applications in rosetta3.4 (ex. make_fragment; abinitio, relax and etc.)? What are these improvements (Speed, Accuracy)?

Thank you very much!

Hi there,

I've been trying to find the definition of the cluster application's -gdtmm flag, and why we might use it over clustering by rmsd (no flag required).
All the examples I've run across use the -gdtmm flag, but again, I'm just not how exactly this is clustering.

Then, following that, when the flag -cluster:sort_groups_by_energy is used, how does it sort them? Does it label the first cluster as the one with the lowest average energy for all the structures in the cluster? It almost seems at odds with clustering by RMSD.

Any ideas?

Dear All,

I'm a new user of Rosetta software and I believe I have the usual questions to ask, but as long as I've searched (manuals and web) I couldn't find satisfying answers.
I have generated 30000 structures with the abInitio protocol in parallel, 100 structures each run taking care of the seed number. Afterwards I've combined the 300 silent outputs with the combine protocol.
then I've clustered all these decoys with the cluster protocol. The results after the clustering were 150 pdbs called c.*.0.pdb which I understood as the best scored structure from each cluster.