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Can anyone suggest to me how to relax a protein with a non-covalent ligand? I want to make sure the ligand-binding site does not change dramatically. In the following scenarios, which one looks reasonable:
1) relax protein with ligand; use movemap to exclude the rotamer of ligand residue
I'm attempting to use Rosetta Antibody Design (RAbD) v2019.35.60890 to design antibodies for a protein whose structure is a trimer.
BACKGROUND: I can successfully run the RAbD protocol on the ful trimer structure from the PDB (6VXX) with the following command:
I am trying to run a basic antibody/antigen design/dock simulaton using RosettaAntibodyDesign (from Rosetta 3.12)
I am using the command:
antibody_designer.macosclangrelease \ -database /path/to/database/ \ -do_dock \ -use_epitope_constraints \ -nstruct 5 -in:file:s complex_renumbered.pdb \ -seq_design_cdrs H1 H2 H3 \ -primary_cdrs H3 \ -mintype relax \ -run_snugdock \ -run_relax \ -out:path:all ./output
I'd like to do something similar to regular Rosetta fold-and-dock but in PyRosetta. I've looked at D060_Folding.py and D100_Docking.py examples and while I (mostly) understand what each is doing, I have no idea how to combine them.
How to get a foldtree with symmetry? (in my case it's just simple C3)
How to combine folding and docking? Just alternate calls to folding.apply(test_pose) and dock_prot.apply(test_pose)? (It can't be that simple...)
I'd like to fold-and-dock a trimeric transmembrane domain. I mostly have the "Fold And Dock" working following the example in demos/public/symmetry_examples/fold-and-dock/. However this is treating the transmembrane helixes as though they are in solvent (so for example any hydrophilic groups always rotate outwards). I'd like to do something which is a combination of "Membrane Abinitio" and "Fold and Dock". Is this possible, and how do I do it?
I'm folding a protein which is a trimeric long helix bundle. I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc). This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves. I'd like to constrain this to extended conformations only.
I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:
I am quite new to Rosetta. I have a very simple questions regarding general concepts about ligand-docking. I am a little bit confused about how to set parameter to ensure that all conformers generated can be tested. Lets say if I have a PDB containing 50 conformers. If I set -nstruct = 1 and run docking.xml with transformer like this (Transform name="predock" chain="X" box_size="20" move_distance="2" angle="20" cycles=“500” repeats=“2” temperature=“5”/>). What does really happen through the docking simulation?
I am a beginner of Rosetta. While I am running ligand-docking toturial (https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial). I encounter an error when run script calculate_ligand_rmsd.py when doing data analysis. This script is used to calculate RMSD of each model comapred with the best model. When I run this script, the error indicated ：