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

This topic has 1 reply, 2 voices, and was last updated 3 years, 8 months ago by Anonymous.

Viewing 1 reply thread

Author

Posts
- February 3, 2021 at 7:44 am #3684
  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
- February 3, 2021 at 10:45 pm #15704
  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.)
Author

Posts

Viewing 1 reply thread

You must be logged in to reply to this topic.