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The problem hasn't been solved
We would like to restrcuture the IL-2 for better binding with receptors - beta and gamma. We used tools to restructure IL2 and get a list of different variants. i.e. a list of PDB files. We hope to use computation method to find out the limited list of best structures before going to lab. So that we can focus on best group first to save time and resource.
I would like to try out ShapeSimilarity and ElectrostaticSimilarity filters that were described in the 3.13 release notes (https://www.rosettacommons.org/docs/latest/release-notes), but the links on that page says it's "Forbidden. This Wiki is set to no-edit mode." I tried adding it to Rosetta script and I get "This element is not expected" error. Would somebody be able to point me to the right direction?
mpiexec -np 8 $ROSETTA_BIN/minimize_ppi.mpi.linuxgccrelease -database $ROSETTA_DATABASE -l pdb.lst
runs each structure in the list 8 times instead of running one structure per processor, thus 8 structures simultaneously. But minimize.mpi.linuxgccrelease distributes the jobs via jd2 and runs 8 structures on 8 processors simultaneously. Any thoughts? Thanks!