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Chemically bound ligand connection error

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Chemically bound ligand connection error

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 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. Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv 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. Database file opened: scoring/score_functions/rama/fd/all.ramaProb Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt Database file opened: scoring/score_functions/omega/ Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt Database file opened: scoring/score_functions/P_AA_pp/P_AA 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. 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

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

using -out:level 500 I found the probable source of the error. 

core.conformation.Conformation: Residue 256 is not a branch point!

core.scoring.elec.FA_ElecEnergy: Warning!  Unable to find countpair representatives for restype LG1

how can I make this residiue a "branch point"? I have the constraint file: 

AtomPair OG 36 P1 256 HARMONIC 1.9 0.01

Angle OG 36 P1 256 O4 256 HARMONIC 1.94080613 0.034906585

Angle CB 36 OG 36 P1 256 HARMONIC 2.19562420 0.034906585



ICOOR_INTERNAL  CONN1  180.000000   68.800000    1.600000   P1    O4    C8

in the params file 

so I dont know how else I need to inform rosetta that residue 256 is a branch point..... please help!! 

Tue, 2019-01-22 14:04


So far I have just used structures from MD simulations which have already "relaxed" around the ligand, then removed the ligand for the dock and design. This does give me different results for different ligands, leading me to believe it could be sufficient, but would like to have all atoms as explicit as possible.

Mon, 2019-02-18 09:55