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Dear Sir and Madam,
When I run such a script "~/rosetta_src_2020.08.61146_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol Design.xml -s some_relaxed_protein.pdb -database ~/rosetta_src_2020.08.61146_bundle/main/database/ -restore_talaris_behavior true -remodel:use_pose_relax true -score:set_weights pro_close 0 cart_bonded 0.5 -nstruct 10 -out:prefix design_" for insertion one amino acid, replacement one original amino acid into another and building additional disulphide I meet with the following error:
I am trying to running RAbD with the following command:
-l design_input.list \
-primary_cdrs H3 \
-graft_design_cdrs H3 \
-seq_design_cdrs H1 H2 \
-paratope H3 \
-mc_total_weight .001 \
-mc_interface_weight .999 \
-nstruct 3 | tee designing.log
I am trying to use Rosetta dock and antibody design modules to design antibody in order to improve the affinity of the antibody to the antigen. Firstly I docked the antibody to the antigen. In this step I got 500 and antibody-antigen complex models and selected top 10 models based on the lowest I_sc energy. Then I ran AntibodyDesign using a command like the follow for each of the 10 complex models:
I came across the Coupled Moves protocol recently and it sounds like an interesting alternative to FastDesign that I've been predominantly using. I tried to implement the CoupledMoves Mover within my RosettaScripts design script, however, I keep coming across the following error:
ERROR: FoldTree:: residue_edge is undefined for root vertex
ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 2317
[0m[0mprotocols.rosetta_scripts.ParsedProtocol: [0m[31m[1m[ ERROR ][0m Exception while processing procotol:
I am using RosettaLigand design protocol to design some mutants, in order to improve binding affinity to a small molecule. When I was using InterfaceAnalyzer, there were 2 values representing binding affinity, interface_delta_X and dG_separated. I want to know the difference between these 2 values and which one I can use during the filter process.
Any suggestion will be appreciated!
I was wondering whether Remodel is currently compatible with the RosettaMP framework? I have a designed membrane protein and I'm trying to alter the sequence of water-exposed loops, which involves a few insertions. I'm using Remodel to do this but haven't been able to run it using the franklin2019 scorefunction.
Here are the flags that I'm using:
I am running some flexible backbone design on a transmembrane four-helix bundle heme protein via RosettaScripts. I'm finding that the membrane residue is moving a lot during design, and I have to optimize the embedding with mp_transform post-design to reposition the mem residue. I have a few questions about this:
I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb.
However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).
Is there any way to runn RAbD while FIXing all the CDRs?