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I'm preparing to start an enzyme redesign project using Rosetta, but the paper I'm supposed to be working off used the older enzdes application, which doesn't seem to be compatible with newer scorefunctions and sampling methods. CoupledMoves seems preferable, and I was hoping to get some recommendations for putting together a ligand docking and design protocol. I have basic familiarity with Rosetta, but since I'm the only person in my lab using it right now, I'd really appreciate any advice to help speed up the process and reduce time spent on trial and error.
I have some questions about using enzyme design application for my system.
1. I have not used RosettaMatch, but I have a rough complex structure of the enzyme with the ligand. Is it fine to use that or I need to use RosettaMatch?
I am trying to use IntearctiveRosetta on windows 10 environment and have zero knowledge about coding.....could anyone help me to solve this error......which comes up when I do a position scan using IntearctiveRosetta.....
Traceback (most recent call last):File "scripts\daemon.py", line 2024, in daemonLoopdoPMutScan()File "scripts\daemon.py", line 503, in doPMutScanos.rename("scanprogress", "scanoutput")WindowsError: [Error 32] The process cannot access the file because it is being used by another process
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 relax my protein with ligands FMN before do further design. I used movemap to exclude the rotamer on FMN. my flag and movemap file looks like below. I also attached my protein_FMN pdb. It takes an extremely long time and it seems like stuck somewhere (I attached the screen shot). Is it normal and anybody knows why? Thanks
# Harmonic runs
Hi, does anyone know how to do alanine scanning for just one protein?
I looked at different movers for RosettaScripts, like ddgScan, AlaScan, and ddg. Can any of these be used for a single protein with no interface? I want to see which protein residues are good targets for mutation.
I am trying to design the binding site of a protein with certain ligands and there is a common error that I encounter with various ligands (not all). The error says "Angle constraint: 0-length bonds". I checked the input structure and there are no atom clashes. I am not sure what is causing this error. If anyone has an idea, it would be a great help.
Thank you !
I was trying to run rosetta match with Rosetta/main/source/bin/match.linuxgccrelease
The match was done successfully with older version of rosetta, but didn't work with Rosetta 3.10. It aborted because of an error of "ERROR: Assertion 'build_sets_[ build_set_id ].restype().has( "1HA" ) failed. ERROR:: Exit from: src/protocols/match/upstream/ProteinUpstreamBuilder.cc line 1210". I was wondering if there's a way to fix this. Many thanks.
I've been playing with the enzyme design binary application using enzymes containing DNA or RNA in the pose. The FlexBB protocol can be activated by setting the flag '-enzdes:flexbb_protocol true'. If no loop file is provided via the flag '-enz_loops_file <file>' the default protocol behavior is to iterate through the pose to identify flexible regions in the structure for loop design. I found that having either DNA /RNA in the pose triggers the following error consistently after cst minimization.