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I am trying to work on the protein-protein interface design using rosetta scripts. I am new to running rosetta scripts. So, I kindly need help on that.
I ran the configure file given in the first step which threw me an error of Nobsub in path. I tried installing bsub and adding paths to the bash file but still wasn't able to proceed further.
Kindly help me out if there are any mistakes or details i may have missed in setting up the run.
Thanks in advance
I'm beginning to play around with CoupledMoves for flexible backbone design and I am unable to get it to alter the protein backbone coniguration.
When I run the tutorial here (https://github.com/Kortemme-Lab/coupled_moves-tutorial) it works. But when I try and apply that (or similar) command to another protein it will deisgn the sequence, but all the output pdbs have no coordinate changes.
Dear Rosetta experts,
I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.
I am working on designing some symmetric structures and am currently using REF2015 + hbnet. In addition, I want to add the buried_unsatisfied_penalty. When I add this term to the score function, it works and can score 'non-symmetrized' structures just fine. However, when I try to score a structure that has been 'symmetrized' I get the following error:
[ ERROR ] UtilityExitException
I am trying to do antibody design with the RosettaAntibodyDesign, but some of my colleagues told me that they fell to obtain successful designers with the RosettaAntibodyDesign (RAbD). They ran the RosettaAntibodyDesign on the crystal structure of an ab-ag complex with a dG_seperate of about -20 REU, and got some designers with dG_seperate of about -40 REU. However, they did experiments including ELISA and SPR and found that these antibody designers did not bind to the antigen at all!