There is a problem executing “rosetta_scripts.static.linuxgccrelease ”

[Anonymous]

import subprocess

def minimize(working_directory):

subprocess.run([rosetta/main/source/bin/rosetta_scripts.static.linuxgccrelease,

f"@{flags_relax.txt}",

f"-parser:protocol",

f"{dock_relax.xml}"',

"-database","rosetta/main/database/],

cwd=str(working_directory))

The above is the program I used.When I use rosetta_scripts.static.linuxgccrelease command to minimize pdb, but the following warning appears and the program cannot be stopped:

ore.import_pose.import_pose: File ‘./10gs_complex.pdb’ automatically determined to be of type PDB

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 1 in file ./10gs_complex.pdb. Best match rsd_type:  PRO:NtermProteinFull

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 2 in file ./10gs_complex.pdb. Best match rsd_type:  TYR

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 6 in file ./10gs_complex.pdb. Best match rsd_type:  TYR

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 7 in file ./10gs_complex.pdb. Best match rsd_type:  PHE

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 8 in file ./10gs_complex.pdb. Best match rsd_type:  PRO

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 10 in file ./10gs_complex.pdb. Best match rsd_type:  ARG

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 11 in file ./10gs_complex.pdb. Best match rsd_type:  GLY

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 12 in file ./10gs_complex.pdb. Best match rsd_type:  ARG

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 13 in file ./10gs_complex.pdb. Best match rsd_type:  CYS

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 16 in file ./10gs_complex.pdb. Best match rsd_type:  LEU

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 17 in file ./10gs_complex.pdb. Best match rsd_type:  ARG

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 18 in file ./10gs_complex.pdb. Best match rsd_type:  MET

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 19 in file ./10gs_complex.pdb. Best match rsd_type:  LEU

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 20 in file ./10gs_complex.pdb. Best match rsd_type:  LEU

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 22 in file ./10gs_complex.pdb. Best match rsd_type:  ASP

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 23 in file ./10gs_complex.pdb. Best match rsd_type:  GLN

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 24 in file ./10gs_complex.pdb. Best match rsd_type:  GLY

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 25 in file ./10gs_complex.pdb. Best match rsd_type:  GLN

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 26 in file ./10gs_complex.pdb. Best match rsd_type:  SER

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 27 in file ./10gs_complex.pdb. Best match rsd_type:  TRP

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 28 in file ./10gs_complex.pdb. Best match rsd_type:  LYS

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 29 in file ./10gs_complex.pdb. Best match rsd_type:  GLU

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 30 in file ./10gs_complex.pdb. Best match rsd_type:  GLU

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 35 in file ./10gs_complex.pdb. Best match rsd_type:  GLU

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discard

 

rotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Transform – transform=======================

protocols.qsar.scoring_grid.GridManager: Found a conformation matching hash: a7de8cb96cb59df62984c05de8d55d8e5c648d80 Loading from grid cache

protocols.ligand_docking.Transform: Considering 1 conformers during sampling

protocols.ligand_docking.Transform: percent acceptance: 250 0.5 250

protocols.ligand_docking.Transform: Accepted pose with grid score: -56

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER HighResDocker – high_res_docker=======================

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.pack_rotamers: built 1389 rotamers at 17 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.pack_rotamers: built 1464 rotamers at 18 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -1015.76 -1015.9

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FinalMinimizer – final=======================

protocols.ligand_docking.ligand_options.FinalMinimizer: Energy prior to minimizing: -1041.68

protocols.ligand_docking.ligand_options.FinalMinimizer: Energy after minimizing: -1249.57

protocols.rosetta_scripts.ParsedProtocol: setting status to success

protocols.jd2.JobDistributor: 10gs_complex_0018 reported success in 6 seconds

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: filling pose from saved copy ./10gs_complex.pdb

protocols.jd2.PDBJobInputter: setting up metal constraints for saved pose copy ./10gs_complex.pdb

core.util.metalloproteins_util: Automatically setting up constraints between metal ions and metal-binding residues.

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: filling pose from saved copy ./10gs_complex.pdb

protocols.jd2.PDBJobInputter: setting up metal constraints for saved pose copy ./10gs_complex.pdb

core.util.metalloproteins_util: Automatically setting up constraints between metal ions and metal-binding residues.

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Transform – transform=======================

protocols.qsar.scoring_grid.GridManager: Found a conformation matching hash: a7de8cb96cb59df62984c05de8d55d8e5c648d80 Loading from grid cache

protocols.ligand_docking.Transform: Considering 1 conformers during sampling

protocols.ligand_docking.Transform: percent acceptance: 211 0.422 289

protocols.ligand_docking.Transform: Accepted pose with grid score: -52

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER HighResDocker – high_res_docker=======================

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.pack_rotamers: built 1061 rotamers at 16 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.pack_rotamers: built 1533 rotamers at 18 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for WER

protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -1020.08 -1022.16

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FinalMinimizer – final=======================

protocols.ligand_docking.ligand_options.FinalMinimizer: Energy prior to minimizing: -1109.73

The files required by the program are in the attachment, and there are log files for running

 

 

 

 

[Anonymous]

There’s nothing intrinsically wrong with those warnings. They’re just telling you that there’s something about your input PDB file (specifically the atom naming) which Rosetta doesn’t like.

It’s hard to say off hand what that might be without seeing the PDB input. But most often it either has to do with hydrogen naming (Rosetta uses an older hydrogen naming convention), or it’s due to using an input from another program which names certain atoms differently than the PDB convention (normally these are the beta-branched amino acids).

I’m not sure if either of those is what’s going on. I’d probably recommend taking a look at your input PDB, and looking at the residues listed at the specified positions (residues numbered starting at 1 from the beginning of the file). Since you’re getting successful output, compare the atom names listed to the atom names listed in the output file. If you find atom names which are in the input but not in the output, those are what are giving you that warning message.

Whether that’s an issue or not depends on what atoms they are, and how critical they are to the structure of the protein. (Rosetta will rebuild “missing” atoms from scratch, so if they’re just hydrogen atoms it’s probably not a big deal, as Rosetta will simply rebuild them in their ideal locations.)

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