Chemically bound ligand connection error

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    • January 2, 2019 at 2:40 am #3066
      Anonymous

        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

      • January 22, 2019 at 10:04 pm #14563
        Anonymous

          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

          and 

          CONNECT P1 

          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!! 

        • February 18, 2019 at 5:55 pm #14578
          Anonymous

            Bump?

            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.

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