Membrane

unable to generate the span file with "mp_span_from_pdb.default.linuxgccrelease" from a PDB file

Category:
Membrane

Dear Users,

I am trying to use the "mp_span_from_pdb.default.linuxgccrelease" binary for generating a "span" file to be used as the input for the "predic_ddg.py" python.

However, I face the following error when I start the command.

I face no issues when trying with the demo pdb file. Yet, when I use my pdb (attached), it crashes with the following error.

Thank you

The error:

Post Situation:

Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol

Category:
Membrane

Dear users,

I am trying to run the RosettaMP application to predict the effect of several mutations on the stability of a membrane protein. I am following this documentation to do that :"https://www.rosettacommons.org/docs/latest/application_documentation/membrane_proteins/RosettaMP-App-MPddG"

However, I can not locate the "compute_ddg.py" in the expected derectory (source/src/python/bindings/app/membrane/compute_ddG.py).

Post Situation:

Relax in membrane pull my protein out of the membrane

Category:
Membrane

Good day,

I am having issues with the mp_relax protocol. I am testing the protocol directly from a PDB crystal structure, and the relax algorithm takes this structure out from the membrane region (as defined by the MEM residue). I am first optimizing the membrane location with the mp_transform (with the -mp:transform:optimize_embedding true option), which positions the protein in the membrane as expected. Then, the relax protocol pulls out the protein from this "correct" membrane position, leaving the protein completely exposed to solvent.

Post Situation:

calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

Category:
Structure prediction
Constraints
Symmetry
Membrane

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

Post Situation:

FastRelax Mover with symmetry, ligand and membrane

Category:
Structure prediction
Symmetry
Membrane

Dear all,

Post Situation:

MPI optimization on TACC stampede2 HPC

Category:
Structure prediction
Loop Modeling
Symmetry
Membrane

Dear community,

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.

Post Situation:

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!

Category:
Membrane

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!

Post Situation:

Membrane-bound relaxation constrained by an ED map

Category:
Membrane

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.

Post Situation: