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I am new to MPI so please correct any misuse of terms. My question is about optimizing for MPI on an HPC or a second (preferred) solution to my issue is to optimize my RAM usage so I don't have to run MPI, serial would actually improve overall models produced anyways.
I am doing an efficiency analylis on the different minimization options in Rosetta using FastRelax, MPRelax and lbfgs_armijo_nonmonotone minimizer on a membrane protein using the franklin2019 score function and I very very often get this error:
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!
I am energy minimising a membrane protein with the RosettaMP framework, but also constraining it to the electron density map.
I am creating the membrane chain vector thinggy by starting with an OPM database style PDB (protein placed ±14 Å xy plane but without the cute membrane marker atoms aren't used) with the usual `pyrosetta.rosetta.protocols.membrane.AddMembraneMover('from_structure')`, but then I am calling `pyrosetta.rosetta.protocols.simple_moves.AlignChainMover()` to move the pose (based on the peptide chain) to a pose in the ccp4 map.
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 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: