RosettaCommons - Enzyme Design

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Memory Leak: Relax Density MPI RAM overusage kills process

mmfarrugia — Sun, 31 Dec 2023 20:02:31 +0000

I am trying to use Rosetta relax to refine my homology modelled enzyme models to my CCP4 maps, but Rosetta RAM usage rockets all the way up to 128 GB after a little less than a minute (regardless of number of processors) and then linux auto-kills it due to RAM overusage. I have watched the htop as the process runs, and I have 128 GB on the system, only 1-2 GB are being used by other processes, but it rockets up from ~ 30% usage all the way up and then dies quite clearly when it runs out of RAM. I have tried running it with 32 or 8 nodes as well, no difference in results.

Indication of RAM overusage killing the process:

mpirun noticed that process rank 5 with PID 0 on node wiestml exited on signal 9 (Killed).

My executable file running the MPI application:

mpirun -np 16 /opt/rosetta/rosetta_src_2021.16.61629_bundle/main/source/bin/relax.linuxgccrelease \
 -database /opt/rosetta/rosetta_src_2021.16.61629_bundle/main/database \
 -in:file:s score_pre4i4b_a2_b2_cat_INPUT_0001.pdb  \
 -relax:fast \
 -relax:jump_move true \
 -edensity:mapfile 4i4b_phases_2mFo-DFc.ccp4 \
 -edensity:mapreso 1.70 \
 -edensity:fastdens_wt 50.0 \
 -symmetry_definition 4i4b_a2_b2.symm \
 -ignore_unrecognized_res \
 -out::nstruct 5 \
 -ex1 -ex2 \

happy to share the full output file if it is useful but there are no errors in the output

Truncated Output:

core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
core.conformation.symmetry.Conformation: Found disulfide between residues 294 720
core.conformation.symmetry.Conformation: current variant for 294 CYS
core.conformation.symmetry.Conformation: current variant for 720 CYS
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
core.conformation.symmetry.Conformation: Found disulfide between residues 294 720
core.conformation.symmetry.Conformation: current variant for 294 CYS
core.conformation.symmetry.Conformation: current variant for 720 CYS
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
core.conformation.symmetry.Conformation: Found disulfide between residues 294 720
core.conformation.symmetry.Conformation: current variant for 294 CYS
core.conformation.symmetry.Conformation: current variant for 720 CYS
core.conformation.symmetry.Conformation: current variant for 294 CYD
core.conformation.symmetry.Conformation: current variant for 720 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 720 to 294
core.conformation.symmetry.Conformation: Found disulfide between residues 294 720
core.conformation.symmetry.Conformation: current variant for 294 CYS
core.conformation.symmetry.Conformation: current variant for 720 CYS
core.conformation.symmetry.Conformation: current variant for 294 CYD
core.conformation.symmetry.Conformation: current variant for 720 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 720 to 294
core.conformation.symmetry.Conformation: Add symmetric chemical bond 294 to 720
core.conformation.symmetry.Conformation: Add symmetric chemical bond 294 to 720
core.conformation.symmetry.Conformation: current variant for 294 CYD
core.conformation.symmetry.Conformation: current variant for 720 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 720 to 294
core.conformation.symmetry.Conformation: Add symmetric chemical bond 294 to 720
core.conformation.symmetry.Conformation: current variant for 294 CYD
core.conformation.symmetry.Conformation: current variant for 720 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 720 to 294
core.conformation.symmetry.Conformation: Add symmetric chemical bond 294 to 720
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
core.conformation.symmetry.Conformation: current variant for 294 CYD
core.conformation.symmetry.Conformation: current variant for 720 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 720 to 294
core.conformation.symmetry.Conformation: current variant for 294 CYD
core.conformation.symmetry.Conformation: current variant for 720 CYD
core.conformation.symmetry.Conformation: Add symmetric chemical bond 720 to 294
core.conformation.symmetry.Conformation: Add symmetric chemical bond 294 to 720
core.conformation.symmetry.Conformation: Add symmetric chemical bond 294 to 720
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.pose.util: [ WARNING ] addVirtualResAsRoot() called but pose is already rooted on a VRT residue ... continuing.
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density map4i4b_phases_2mFo-DFc.ccp4
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:  Setting resolution to 1.7A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'4i4b_phases_2mFo-DFc.ccp4'
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity:      extent: 200 x 174 x 180
core.scoring.electron_density.ElectronDensity:      origin: 177 x 223 x 125
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 540 x 540 x 540
core.scoring.electron_density.ElectronDensity:     celldim: 226.082 x 226.082 x 226.082
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.0733866
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
core.scoring.electron_density.ElectronDensity: Effective resolution = 1.7
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.0637226,3.25267]
core.scoring.electron_density.ElectronDensity: Bin 1:  B(C/N/O/S)=0 / 0 / 0 / 8.60156  sum=(0,0)
core.scoring.electron_density.ElectronDensity: Bin 1:  B(C/N/O/S)=0 / 0 / 0 / 8.60156  sum=(0,0)
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
Got some signal... It is:15
Signal 15 (SIGTERM) means that the process was terminated.  This usually means that something external to Rosetta, such as a queing system, aborted the process (e.g. due to a time or resource limit).
--------------------------------------------------------------------------
mpirun noticed that process rank 5 with PID 0 on node wiestml exited on signal 9 (Killed).

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Post Situation:

Error when running the CstfileToTheozymePDB Application

jkoch19 — Mon, 18 Dec 2023 16:34:32 +0000

Hello,

I am relatively new to Rosetta, and i am trying to generate a constraint file (.cst) with my catalytic amino acid and ligand defined, that i am going to use to search against a PDB database. However, no matter how hard i try i keep obtaining this error:

protocols.toolbox.match_enzdes_util.InvrotTree: A total of 112 unique definitions of the invrot tree exist.
protocols.toolbox.match_enzdes_util.InvrotTree: Writing definition 1 to file PDB_Model_RD-2.cst_1.pdb...
protocols.toolbox.match_enzdes_util.InvrotTree: 100 invrots for list 0, 54 invrots for list 1, 15 invrots for list 2, 10 invrots for list 3, 234 invrots for list 4, 10 invrots for list 5,

ERROR: Assertion `serial_to_serial_with_ter.count(ai.connected_indices[ c_index ] )` failed.
ERROR:: Exit from: src/core/io/pdb/pdb_writer.cc line: 616

[ ERROR ]: Caught exception:

File: src/core/io/pdb/pdb_writer.cc:616
[ ERROR ] UtilityExitException
ERROR: Assertion `serial_to_serial_with_ter.count(ai.connected_indices[ c_index ] )` failed.

I appreciate all help i can get at this point! Thank you

Attachment	Size
Params file of my ligand	7.83 KB
CST File	3.38 KB
Rosetta Crash log	1.31 KB

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Forums:

Rosetta++ - Applications

Match: Outputs with 0 hits for cst and clashes with sidechains

uka147 — Wed, 08 Nov 2023 14:11:57 +0000

Hi all,

I was running the Match application and :
1. I noticed that some outputted PDBs are annotated in the log file as follows (I am using cloudPDB as output format):

protocols.match.output.PDBWriter: (0) beginning writing cloud for group 471
protocols.match.output.PDBWriter: (0) 0 upstream hits and 0 downstream hits for geom cst 1
protocols.match.output.PDBWriter: (0) 0 upstream hits and 0 downstream hits for geom cst 2
protocols.match.output.PDBWriter: (0) A total of 1 models were written for match group 471 in 1 files.

Indeed, after checking some of these outputs, I found that the cst blocks are not (fully) satisfied by the models created.
Is normal behaviour for the match outputter to create cloud groups and models even when it finds no hits? Am I missing something?
Is there a way to filter out (or even better, to not output) these groups showing no hits for my cst?

2. I wanted to play with the collision filters parameters. In particular, I find that in most outputs I have big clashes of my substrate with the side chains of my scaffold. I would like to filter out all matches showing upstream-downstream clashes. Though, I dont seem to manage. By adding, removing any type of collision-related flag or by changing their values, no match gets actually filtered.
About the collision filter flags: does "upstream" refer to all residues of the scaffold or only to the newly introduced residues based on the cst? And are the sidechains included or just collisions with the backbone are filtered out?
By using the flag "-bump_tolerance 0", am I filtering out clashes with both sidechains and backbone of the whole scaffold?
Is there a combination of flags and/or their values that would help me achieve what I want or, at least, matches with small/less clashes with the sidechains?
The output I get in the logfile is the one below:

Created UpstreamCollisionFilter
core.scoring.etable: (0) Starting energy table calculation
core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: (0) Finished calculating energy tables.
Created UpstreamDownstreamCollisionFilter
...
protocols.match.output.MatchProcessor: (0) No matches failed any filter.

Thank you in advance!

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Post Situation:

Are catalytic residues mutatable?

uka147 — Thu, 26 Oct 2023 10:49:54 +0000

Hi all,

I was running the integration test of the enzyme design (main/tests/integration/tests/enzdes). According to the fifth constraint block in the cstfile at position Trp100 residues WFY with atom type aroC are allowed. However within 150 output structures I never observe a mutation away from the native Trp. In contrast, residue Ser98 is variable in the results (only has backbone constraints). Similarly, I never observe any mutation away from a native catalytic sidechain in my own project.

Is this expected behavior? I am presuming that due to the prior optimization of the catalytic interactions, the mutation of a catalytic residue is highly unfavored and therefore no mutation of these is ever observed but I'm not sure about this.

Do you know if it is by principle possible that a catalytic residue (sidechain involved in catalysis) is mutated by enzyme_design, when listing different amino acids in the cst file as possible residues?

Thanks!

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Post Situation:

Solved

Rosetta Design: Non-canonical amino acid substrate not accepted

Friedrich Ehinger — Fri, 04 Aug 2023 07:09:55 +0000

I experience difficulties when submitting an enzyme PDB file with the
substrates AMP and a non-proteinogenic amino acid to the RosettaDesign webserver.
AMP is well accepted but problems arise with the amino acid substrate.

If I name the amino acid with a common identifier such as PHE in PyMOL, its chemical
structure is changed towards e.g. Phe during the design calculations. If I name it differently such as XYX,
the substrate is discarded in calculations. How should I name the molecule so that
it is kept in enzyme design calculations and not chemically modified during the pipeline?

Thanks in advance!

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Post Situation:

Converting all residues to poly-Gly/Ala

jtpi6174 — Tue, 09 May 2023 21:14:36 +0000

Hey, I am pulling my hair out over this. I am trying to convert all residues in a protein to poly-Gly/Ala (for example 1ae1.pdb) but cannot find the Rosetta function to do so. I am replicating a paper where they included code and output, the output appears to be typical Rosetta output (the .pdbs are like 3tzc___1.pdb) which I am assuming were generated with a Rosetta function.

I have looked in Rosetta/tools/protein_tools/ and other folders within Rosetta/demos/public/ and /tutorials/ but cannot for the life of me find out how to convert a PDB to all Gly or Ala.

I have been looking at `phenix.pdbtools` too but that only truncates (i.e. doesn't change the res names to GLY or ALA in the PDB). The author of the paper used both Phenix and Rosetta so I am assuming it is in Rosetta this function occurs.

Does anyone know the Rosetta function to convert a given structure to poly-Gly/Ala please or what function/programme does so? I am not far from programming something myself in Python as it is frustrating, thank you.

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Rosetta 3 - General

Post Situation:

Solved

Which application/mover should I use to evaluate the ddg between apo enzyme and enzyme binding with transition state?

JasonIsaac — Thu, 23 Feb 2023 02:36:24 +0000

Hi everyone:

I used Enzyme Design application to get a series of enzymes with ligand(transition state of my target reaction). Now I want to inspect the free energetic change upon the protein transition state binding.

So I first look into the ddg_monomer application, and I find this application is suitable for comparing ddg energy between wild-type protein and its mutant structures. This can't meet my needs.

I am wondering if there is any application can evaluate the ddg between apo enzyme and enzyme binding with transition state? Any suggestions would help. Thanks for you time and effort.

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Rosetta 3 - General

Post Situation:

Designing Feasible Backbones

csvajda — Sat, 13 Aug 2022 15:08:13 +0000

Hi there!

In the process of trying to learn protein design for the last year and a half I have been focusing on using the newest and best tools for designing sequences. And the tools for designing a sequence to match a conformation seem to be reaching a level, such as with the protein MPNN release, that they're almost plug and play.
But I've come to realize that just because a backbone looks realistic doesn't mean it is. As a proxy to check this, when designing a sequence with either trRosetta or MPNN and then running it through a program like AlphaFold or RoseTTAfold I can see pretty quickly if the structure/sequence are in the ballpark or are totally unfoldable.
My question is this: how does one avoid the process or blind trial and error when trying to get a backbone that fits the needs of a project but is also in realistic conformation space? Is it truly a numbers game of eyeballing realistic structures and repeating? Or are there tools and metrics to do the grunt work prior to sequence design?

any answers would be greatly appreciated!

-Cooper Svajda

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Post Situation:

Benchmarking Rosetta DDG Methods

sareeves96 — Fri, 29 Jul 2022 16:55:08 +0000

Hi,

I am looking to benchmark Rosetta ddg / single-point mutation stability calculations against some emerging machine learning methods. There doesn't seem to be a consensus on which methods are most broadly applicable; from the literature I have read, it seems that choices of applications and flags are almost arbitrary. Aside from the 'default' protocols posted on the documentation webpages for ddg_monomer and cartesian_ddg, has anyone established a reliable workflow that could be tested outside of ProTherm mutations? In particular, are there any obvious "higher-resolution" cartesian_ddg protocols expected to outperform the aforementioned default baselines?

Thanks!

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