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Chemically bound ligand connection error

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Chemically bound ligand connection error
#1

I am following the protocol for Relax Around A Chemically Bound Ligand

/path/rosetta/3.9/main/source/bin/relax.static.linuxgccrelease -s AcpP-TesA-C8.pdb -in:file:fullatom -extra_res_fa ./LG.params -cst_fa_file chemical_bond.cst -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -ex1 -ex2 -use_input_sc -flip_HNQ -no_optH false -overwrite 

and I get the error 

core.init: Rosetta version: rosetta.binary.linux.release-171 r171 2018.09+release.333d996 333d99699777cd6a50d1c1736bacd689f8f1d1df https://www.rosettacommons.org 2018-02-27T09:57:00.705373

core.init: command: /software/repo/moleculardynamics/rosetta/3.9/main/source/bin/relax.static.linuxgccrelease -s AcpP-TesA-C8.pdb -in:file:fullatom -extra_res_fa ./LG.params -cst_fa_file chemical_bond.cst -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -ex1 -ex2 -use_input_sc -flip_HNQ -no_optH false -overwrite

core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1433228123 seed_offset=0 real_seed=-1433228123

core.init.random: RandomGenerator:init: Normal mode, seed=-1433228123 RG_type=mt19937

core.init: Resolved executable path: /software/repo/moleculardynamics/rosetta/3.9/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/relax.static.linuxgccrelease

core.init: Looking for database based on location of executable: /software/repo/moleculardynamics/rosetta/3.9/main/database/

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015

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/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.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 604 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 1.02 seconds.

basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb

basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.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

core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop

protocols.relax.FastRelax: ================== Using default script - no constraint ramping ==================

core.scoring.constraints.util: Constraint choice: chemical_bond.cst

protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter

protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs

protocols.jd2.PDBJobInputter: pushed AcpP-TesA-C8.pdb nstruct index 1

protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... 

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: filling pose from PDB AcpP-TesA-C8.pdb

core.import_pose.import_pose: File 'AcpP-TesA-C8.pdb' automatically determined to be of type PDB

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ALA:CtermProteinFull 77

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 255

core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 256 with connection point 1

 

I followed the instructions, adding connect and ICOOR lines to params, and provided information in cst file, so I'm not sure why a residue connection cant be found.

I have attached the cst, params, and input file below

AttachmentSize
AcpP-TesA-C8.pdb.txt197.84 KB
chemical_bond.cst_.txt154 bytes
LG.params.txt7.53 KB
Post Situation: 
Tue, 2019-01-01 18:40
tsztain