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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!
The MHC Epitope energy (mhc_epitope) alogrithm (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/MHCEpitopeEnergy) is for deimmunization of epitopes. However I cannot understand how to use it.
I used the pdb file 2b3p.pdb and the score controlling script in the introduction webpage as the inputs and run the following command:
I tried to follow the antibody design protocol from the Nature protocol articles but unfortunately I keep getting the following error when I try it:
core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard
This is my command line:
antibody.default.linuxgccrelease -ignore_unrecognized_res -fasta antibody_chains.fasta
and this is the content of ROSETTA_CRASH.log:
Hello all, I am using the antibody.mpi.linuxgccrelease to model multiple antibodies. Most work fine but about 10% are failing with weird error messages. I have tried everything to figure out the problem but am having no luck. These antibodies are clinical molecules, and so I feel like my failure rate is pretty high, and I'm probably doing something wrong. There is not a lot of documentation about the (newer) antibody homology modelling application and so I am a little bit at a loss as what to do to make the program more robust. Thanks as usual for all your help!!!
I am following the protein design steps presented in the Dr Mieler lab. One of the steps is to generate resfile with define_interface.py script. I checked my rosetta/tools/protein tools/scripts path, but there is not such a file. Where can I find this script?
I'm running running a pilot ROSETTA script to get the GreedyOptMutation mover with the ddg filter to work. But I get this error message;
ERROR: ERROR: No acceptable mutations found. All possible mutations failed at least one filter!
Any ideas on how to get the filter to allow trajectories with mutations that improve ddG and increases affinity between the 2 proteins contained in the .pdb?
My .xml looks like this:
I am trying to design a helical linker between two strongly interacting subunits that connects their termini using RosettaRemodel.
I am running remodel with the following flags in mpi mode and get the desired output (around 2-4 structures with -num_trajectory 32). However when I increase -num_trajectory to e.g. 1000 I still get only around 2-4 strucures out (named 1.pdb 2.pdb ...). while computation time increases drastically.