Error while running RosettaLigand

This topic has 4 replies, 3 voices, and was last updated 11 years, 4 months ago by Anonymous.

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- July 30, 2013 at 9:51 am #1678
  Anonymous
  Hi,everybody!!!
  I am attempting to use the RosettaLigand application to Docking a ligand and protein, this is what I see:
  
  core.init: Mini-Rosetta version unknown from unknown
  core.init: command: /home/ryhon/workspace/rosetta34/build/src/debug/linux/2.6/64/x86/gcc/4.3/ligand_dock.default.linuxgccdebug @ligand_dock/TestSet/1EX7/flags.txt
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=290165452 seed_offset=0 real_seed=290165452
  core.init.random: RandomGenerator:init: Normal mode, seed=290165452 RG_type=mt19937
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
  basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
  basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
  basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
  basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
  basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN6_mem_env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_mem_env_log.txt
  basic.io.database: Database file opened: scoring/score_functions/MembranePotential/memcbeta_den.txt
  basic.io.database: Database file opened: scoring/score_functions/MembranePotential/mem_pair_log.txt
  basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
  basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
  basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
  basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
  core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction.
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6226 residue types
  core.io.pdb.file_data: [ WARNING ] discarding 15 atoms at position 187 in file ligand_dock/TestSet/1EX7/1EX7_NoWater.pdb. Best match rsd_type: 5GP
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C9 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C10 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O8 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: P1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O2 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C9 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C10 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O8 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: P1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O2 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C9 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C10 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O8 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: P1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O2 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C9 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C10 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O8 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: P1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O2 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C9 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O5 on residue 5GP 187
  ……
  
  Do you have any ideas as to what we might be doing wrong? Thank you in advanced!
  Ryhon Wang
- July 31, 2013 at 3:20 am #9158
  Anonymous
  EveryBody!!! Help!!!
  
  Why show
  
  “core.io.pdb.file_data: [ WARNING ] discarding 15 atoms at position 187 in file ligand_dock/TestSet/1EX7/1EX7_NoWater.pdb. Best match rsd_type: 5GP”
  
  when rosettaligand init native pdb and show comments
  
  “
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C9 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C10 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O8 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: P1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O2 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O7 on residue 5GP 187
  “
  
  These errors may be just not finding discarded 15 atoms. Last, RosettaLigand repeat
  
  “
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C9 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C3 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: N5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O5 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: C10 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O8 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: P1 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O2 on residue 5GP 187
  core.conformation.Conformation: [ WARNING ] missing heavyatom: O7 on residue 5GP 187
  “
  again and again finally show Error!!!
  
  I dock 30 cases, 9 cases show similary error for example above in my testset but other 10 cases running is well. The running script is same.
  
  Any help would be greatly appreciated.
- July 31, 2013 at 8:00 pm #9161
  Anonymous
  My guess is that you’re having problems with atom naming. The default behavior of molfile_to_params.py is to rename the atoms. You can attempt to control this with the –keep-names option, but depending on the atom names, it might do the renaming anyway. (It should tell you in the output if it’s renaming the atoms.)
  
  The way Rosetta matches atoms in the PDB file to the params file is with the atom names. If the atoms don’t match, Rosetta will discard the atoms, and do it’s best to rebuild them. molfile_to_params.py should also output a PDB file of the ligand – that should have all the atoms appropriately named, and in their original coordinates. Usually I will use a text editor to replace the ligand coordinate lines in the input PDB with the PDB that was output by molfile_to_params.py.
- August 1, 2013 at 2:05 am #9163
  Anonymous
  you should attach your .params file for ligand
- August 9, 2013 at 2:36 am #9188
  Anonymous
  Thanks rmoretti and skipper a lot, Let me try you advice!!!
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