MakeRotLib – Rosetta Commons

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- July 26, 2019 at 9:18 am #3205
  Anonymous
  I have a about MakeRotLib quenstion:
  
  when I run $ROSETTA3/bin/MakeRotLib.static.linuxgccrelease -database $ROSETTA3_DB -options_file C40.in，Error is as follows：
  
  basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
  
  basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
  
  basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
  
  basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
  
  basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
  
  core.chemical: [ WARNING ] protein residue C40 is not explicitly listed as either L or D in its params file.
  
  core.chemical: [ WARNING ] To avoid seeing this warning in the future, add “L_AA”, “D_AA”, or “ACHIRAL_BACKBONE” to the “PROPERTIES” line of the params file.
  
  core.chemical: [ WARNING ] protein residue Dap is not explicitly listed as either L or D in its params file.
  
  core.chemical: [ WARNING ] To avoid seeing this warning in the future, add “L_AA”, “D_AA”, or “ACHIRAL_BACKBONE” to the “PROPERTIES” line of the params file.
  
  core.chemical: [ WARNING ] protein residue Cit is not explicitly listed as either L or D in its params file.
  
  core.chemical: [ WARNING ] To avoid seeing this warning in the future, add “L_AA”, “D_AA”, or “ACHIRAL_BACKBONE” to the “PROPERTIES” line of the params file.
  
  ERROR: dont add residue bonds more than once!
  
  ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1448
  
  BACKTRACE:
  
  [0x5d62318]
  
  [0x57a6345]
  
  [0x5761914]
  
  [0x57669fd]
  
  [0x56f37b0]
  
  [0x56fefb3]
  
  [0x56e7224]
  
  [0x56e9b17]
  
  [0x56e8b1c]
  
  [0x4454a21]
  
  [0x445514b]
  
  [0x44d575c]
  
  [0x44e6036]
  
  [0x44db2c5]
  
  [0x48e163b]
  
  [0x44d7194]
  
  [0x44a2ace]
  
  [0x44a7967]
  
  [0x44a9366]
  
  [0x44a95cb]
  
  [0x44bf7da]
  
  [0x44c04a2]
  
  [0x44c0ce2]
  
  [0x1d7db94]
  
  [0x627b3a]
  
  [0x4118a8]
  
  [0x625a934]
  
  [0x62741d]
  
  caught exception
  
  File: src/core/chemical/ResidueType.cc:1448
  
  [ ERROR ] UtilityExitException
  
  ERROR: dont add residue bonds more than once!
- July 26, 2019 at 10:00 pm #14853
  Anonymous
  The problem is somewhere in your noncanonical amino acid’s params file. You’ve got duplicated bonds declared between atoms in the residue.
- April 12, 2020 at 3:01 pm #15237
  Anonymous
  Hi
  I am trying to convert a mol2 file to params file using mol2genparams.py script. The mol2params conversion appears to work (please see attached log file) but when I run rosetta_scripts to perform GAliganddocking, it throws up an error “dont add residue bonds more than once”. I have looked at the params file but can’t see any obvious duplications. I am following the protocol outlined for generating mol2 file for GAliganddocking at this location. https://www.rosettacommons.org/docs/latest/GALigandDock-Preprocessing
  
  The .params file is uploaded as a txt file. I would deeply appreciate any help. I have been at it for a week and just can’t seem to find a work around. I have tried to generate mol2 file from different sources, also tried starting from SMILES, pdb and mol but ended up with the same result.
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