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Error while running RosettaLigand

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Error while running RosettaLigand
#1

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

Post Situation: 
Tue, 2013-07-30 02:51
Ryhon Wang

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.

Tue, 2013-07-30 20:20
Ryhon Wang

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.

Wed, 2013-07-31 13:00
rmoretti

you should attach your .params file for ligand

Wed, 2013-07-31 19:05
skipper

Thanks rmoretti and skipper a lot, Let me try you advice!!!

Thu, 2013-08-08 19:36
Ryhon Wang