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
| Attachment | Size |
|---|---|
 AcpP-TesA-C8.pdb.txt | 197.84 KB |
| chemical_bond.cst_.txt | 154 bytes |
| LG.params.txt | 7.53 KB |
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!!
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.