Typical relax options not applied in relax.mpi.linuxiccrelease??

This topic has 11 replies, 3 voices, and was last updated 7 years, 2 months ago by Anonymous.

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- February 27, 2017 at 7:35 pm #2592
  Anonymous
  I am having some difficulty applying Relax using the prebuilt Rosetta 3.7 on TACC:
  
  ibrun $TACC_ROSETTA_BIN/relax.mpi.linuxiccrelease
  
        -database /work/04738/dweis/rosetta_database
  
        -in:path /home1/04738/dweis/E5
  
        -in:file:s 4lgp.B.pdb
  
        -relax:constrain_relax_to_start_coords
  
        -relax:ramp_constraints false
  
        -ex1
  
        -ex2
  
        -use_input_sc
  
        -flip_HNQ
  
        -no_optH false
  
        -nstruct 1
  
        -out:path /work/04738/dweis/E5
  
        -out:file:silent 4lgp.B.relax.o
  
        -out:file:scorefile 4lgp.B.relax.sc
  
        -show_unused_options
  
        -overwrite
  
        &> $HOME/E5/4lgp.B.relax.log
  
  Reading the log indicates that
  
  WARNING: The following options have been set, but have not yet been used:
  
  -out:overwrite
  
  -packing:flip_HNQ
  
  -packing:no_optH false
  
  -packing:use_input_sc
  
  This is odd, becasue these options seem to work fine on relax.macosclangrelease. Any ideas?
- February 27, 2017 at 7:44 pm #12162
  Anonymous
  The set-but-unused message is a (relatively) recent addition, so if you have an older version on your Mac it might not tell you that you’ve set options which aren’t being used. (The support for this message is also application-specific, so some applications may not print the message, even if you have unused options. — In your case, though, all of those options should be read by relax, so it’s not specifically a version issue.
  
  Instead, what’s probably happening is that there’s some other issue that’s going on that means the options aren’t being read. In particular, if Rosetta thinks there aren’t any input structures, it won’t attempt to run the protocol, and so may not read some of the options which control how the protocol runs. In particular, if you’re re-running a commandline where all the output has already been finished, it may not read any of input options.
  
  Again, this is probably not what’s happening in your case, as you have -out:overwrite. Instead, there’s probably some other error which is occuring in the run. — Take a closer look at your tracer output and see if it’s reporting an error elsewhere. In particular, take a look at the locations where it reports on which structures it’s running on.
- February 27, 2017 at 7:44 pm #12683
  Anonymous
  The set-but-unused message is a (relatively) recent addition, so if you have an older version on your Mac it might not tell you that you’ve set options which aren’t being used. (The support for this message is also application-specific, so some applications may not print the message, even if you have unused options. — In your case, though, all of those options should be read by relax, so it’s not specifically a version issue.
  
  Instead, what’s probably happening is that there’s some other issue that’s going on that means the options aren’t being read. In particular, if Rosetta thinks there aren’t any input structures, it won’t attempt to run the protocol, and so may not read some of the options which control how the protocol runs. In particular, if you’re re-running a commandline where all the output has already been finished, it may not read any of input options.
  
  Again, this is probably not what’s happening in your case, as you have -out:overwrite. Instead, there’s probably some other error which is occuring in the run. — Take a closer look at your tracer output and see if it’s reporting an error elsewhere. In particular, take a look at the locations where it reports on which structures it’s running on.
- February 27, 2017 at 7:44 pm #13204
  Anonymous
  The set-but-unused message is a (relatively) recent addition, so if you have an older version on your Mac it might not tell you that you’ve set options which aren’t being used. (The support for this message is also application-specific, so some applications may not print the message, even if you have unused options. — In your case, though, all of those options should be read by relax, so it’s not specifically a version issue.
  
  Instead, what’s probably happening is that there’s some other issue that’s going on that means the options aren’t being read. In particular, if Rosetta thinks there aren’t any input structures, it won’t attempt to run the protocol, and so may not read some of the options which control how the protocol runs. In particular, if you’re re-running a commandline where all the output has already been finished, it may not read any of input options.
  
  Again, this is probably not what’s happening in your case, as you have -out:overwrite. Instead, there’s probably some other error which is occuring in the run. — Take a closer look at your tracer output and see if it’s reporting an error elsewhere. In particular, take a look at the locations where it reports on which structures it’s running on.
- March 1, 2017 at 3:37 pm #12172
  Anonymous
  OK, I dug into this a little bit further, ran my log at 400 level on both Mac (2016.32.58837) and TACC (3.7). In both cases, I do get an output PDB and score file in both cases.
  
  The only other warning lines in the log that I can find are
  
  core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 116
  
  core.io.pdb.file_data: (1) [ OPT-H WARNING ] heavyatom chi angle change: chidev= 180.000 chino= 2 position: 71 ASN ASN
  
  There are no lines containing error messages.
  
  relax.macosclangrelease does not choke on ASN 71.
  
  Am I just running into some subtle difference between the logging output generated by mpi.relax and relax?
- March 1, 2017 at 3:37 pm #12693
  Anonymous
  OK, I dug into this a little bit further, ran my log at 400 level on both Mac (2016.32.58837) and TACC (3.7). In both cases, I do get an output PDB and score file in both cases.
  
  The only other warning lines in the log that I can find are
  
  core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 116
  
  core.io.pdb.file_data: (1) [ OPT-H WARNING ] heavyatom chi angle change: chidev= 180.000 chino= 2 position: 71 ASN ASN
  
  There are no lines containing error messages.
  
  relax.macosclangrelease does not choke on ASN 71.
  
  Am I just running into some subtle difference between the logging output generated by mpi.relax and relax?
- March 1, 2017 at 3:37 pm #13214
  Anonymous
  OK, I dug into this a little bit further, ran my log at 400 level on both Mac (2016.32.58837) and TACC (3.7). In both cases, I do get an output PDB and score file in both cases.
  
  The only other warning lines in the log that I can find are
  
  core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 116
  
  core.io.pdb.file_data: (1) [ OPT-H WARNING ] heavyatom chi angle change: chidev= 180.000 chino= 2 position: 71 ASN ASN
  
  There are no lines containing error messages.
  
  relax.macosclangrelease does not choke on ASN 71.
  
  Am I just running into some subtle difference between the logging output generated by mpi.relax and relax?
- July 28, 2017 at 2:07 pm #13636
  Anonymous
  Dear Rosettaer
  
  I am working on relax my PDB using folllowing script:
```
~/linux_program/rosetta/main/source/bin/relax.default.linuxgccrelease -s 3v2a.pdb -out:suffix _flag_input_relax @flag_input_relax -ignore_unrecognized_res
```
  It produces two PDB for me, but during process and in log file it shows these warnings:
  
  core.chemical.GlobalResidueTypeSet: Total time to initialize 0.373759 seconds.
  
  core.import_pose.import_pose: File ‘3v2a.pdb’ automatically determined to be of type PDB
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 11
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 11
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 11
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 11
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 13
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 13
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 13
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 13
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 33
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 33
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 33
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 33
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 33
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 37
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 37
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 37
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 44
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 44
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 44
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 45
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 45
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 45
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 45
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 45
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 45
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 51
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 51
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 51
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 51
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 52
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 52
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 52
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 52
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 72
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 72
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 72
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 72
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 75
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 75
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 75
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 76
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 76
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 76
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 76
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 109
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 109
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 109
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 109
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 136
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 136
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 136
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 136
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 136
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 136
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 140
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 140
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 140
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 140
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 143
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 143
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 143
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 143
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 155
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 155
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 155
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 155
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 155
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 155
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 158
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 158
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 158
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 158
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 172
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 172
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 173
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 173
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 173
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 173
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 179
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 179
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 179
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 179
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 179
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 179
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 180
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL 180
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 183
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 183
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 183
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PHE:CtermProteinFull 185
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU:NtermProteinFull 186
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU:NtermProteinFull 186
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU:NtermProteinFull 186
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU:NtermProteinFull 186
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 189
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 189
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 189
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 189
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: SD on residue MET 191
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue MET 191
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 196
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 196
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 196
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 196
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 196
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 257
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 257
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 274
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 274
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 274
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 274
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 280
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:CtermProteinFull 280
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:CtermProteinFull 280
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:CtermProteinFull 280
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:CtermProteinFull 280
  
  Can you help me, does these warning impact on my output? or is just normal?
  
  Also, I think my REU are very high. This is my score.sc:
  
  SEQUENCE:
  
  SCORE: total_score coordinate_constraint dslf_fa13 fa_atr fa_dun fa_elec fa_intra_rep fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb omega p_aa_pp pro_close rama ref yhh_planarity description
  
  SCORE: 1524.748 628.449 1112.222 -1168.662 343.962 -126.654 3.262 185.174 637.631 -19.803 -83.953 -16.800 -24.389 84.971 -37.775 2.379 10.384 -6.118 0.467 3v2a_crystal_0001
  
  SCORE: 1527.549 635.786 1102.999 -1167.901 346.881 -127.537 3.251 189.020 636.903 -18.907 -83.753 -17.212 -23.666 83.638 -38.812 2.300 10.152 -6.118 0.525 3v2a_crystal_0002
  
  I look forward hearing from you.
  
  ALI
  - August 3, 2017 at 4:01 pm #13641
    Anonymous
    If you’re loading a from-wwPDB file, those sorts of warning messages are common, especially for long-chain, surface-exposed residues like you have there. These sorts of residues might not have well-resolved atoms in their sidechains, so the coordinates for those atoms might not be present in the PDB file (as there’s no experimental evidence for where they should be). Rosetta will automatically rebuild the positions of the sidechains, putting the missing atoms in the most likely place based on where the rest of the protein is.
    
    Regarding your high energies, you can look at the term breakdown to see that a large amount of that positive energy is coming from the coordinate_constraint and dslf_fa13 terms. The coordinate_constraint energy is coming from the constraints you’ve added to the relax — I wouldn’t include that in considering how good the structure is (as it’s an “artificial” energy that’s been added).
    
    The bigger issue is the dslf_fa13 term. This is the disulfide energy, and it being high means that you have rather poor disulfide geometry in your proteins. I’d take a look at the structures and see if you can spot the bad disulfides. It might be that Rosetta is picking something as a disulfide that shouldn’t be, or something is “stuck” in a bad spot. You might want to try deleting the sidechain atoms of the disulfide residues (with a text editor) and letting Rosetta rebuild them from scratch before the relax (like it does with the other missing atoms). This may help with fixing the geometry.
- March 1, 2017 at 8:55 pm #12175
  Anonymous
  Both relax and relax.mpi should be running basically the same code, aside from the job distribution across the multiple processors. So I’m guessing if you’re getting issues, it’s related to that – I’m guessing for some reason Rosetta isn’t able to set up the MPI environment properly, and then exiting quickly because of it.
  
  I’d take a closer look at the log from your MPI runs, and see if there’s any MPI-related errors or messages which might indicate issues – take a look at the cluster control system (SLURM?) logs as well, to see if there’s some issue with allocating processors.
  
  MPI logs can sometimes be hard to decipher, as all the processes are trying to write to the same file at once, leading to gibberish. You might want to try re-running things with the `-mpi_tracer_to_file <filename_prefix>` option, which will put the tracer output from each MPI node into its own file.
- March 1, 2017 at 8:55 pm #12696
  Anonymous
  Both relax and relax.mpi should be running basically the same code, aside from the job distribution across the multiple processors. So I’m guessing if you’re getting issues, it’s related to that – I’m guessing for some reason Rosetta isn’t able to set up the MPI environment properly, and then exiting quickly because of it.
  
  I’d take a closer look at the log from your MPI runs, and see if there’s any MPI-related errors or messages which might indicate issues – take a look at the cluster control system (SLURM?) logs as well, to see if there’s some issue with allocating processors.
  
  MPI logs can sometimes be hard to decipher, as all the processes are trying to write to the same file at once, leading to gibberish. You might want to try re-running things with the `-mpi_tracer_to_file <filename_prefix>` option, which will put the tracer output from each MPI node into its own file.
- March 1, 2017 at 8:55 pm #13217
  Anonymous
  Both relax and relax.mpi should be running basically the same code, aside from the job distribution across the multiple processors. So I’m guessing if you’re getting issues, it’s related to that – I’m guessing for some reason Rosetta isn’t able to set up the MPI environment properly, and then exiting quickly because of it.
  
  I’d take a closer look at the log from your MPI runs, and see if there’s any MPI-related errors or messages which might indicate issues – take a look at the cluster control system (SLURM?) logs as well, to see if there’s some issue with allocating processors.
  
  MPI logs can sometimes be hard to decipher, as all the processes are trying to write to the same file at once, leading to gibberish. You might want to try re-running things with the `-mpi_tracer_to_file <filename_prefix>` option, which will put the tracer output from each MPI node into its own file.
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