Hello Rosetta people,
I performed a protein protein docking of a protain A + ligand A (74 atoms) noted as binary_complex to protein B, and got warning of missing atoms, still could get docked P-P poses, however, the ligand is not intact, some atoms missed in the output binary_complex. I also added the -ignore_unrecognized_res flag in the command.
Then I parameterized my ligand using molfile_to_params.py to generate LIG.pdb and LIG.params, copied and pasted the coordiantes of LIG.pdb to my binary_complex. I also added the flag "-extra_res_fa LIG.params" in the commond line while performing docking_protocol.static.linuxgccrelease, then I got error massge for missing atoms. (all atoms of my ligand) and calculation killed. No poses were generated at this time.
Can someone instruct how to solve this issue?
-ignore_unrecognized_res is only going to work if the three letter code of the residue is unknown. If Rosetta knows what the residue should be, it won't ignore it, even if the atoms are incomplete.
How to fix it depends on whether you want to include the residue with the error or not. If you don't care about the residue, your best bet is to use a text editor to manually delete those ATOM lines from the input files.
If you want the residue to be present, then you need to fix it such that you have all the atoms. To some extent this depends on why Rosetta isn't finding all the atoms. If it's because you have an incomplete set of atoms, then you'll need to figure out why your upstream process is not outputting all the atoms, or to figure out what the atom coordinates should be.
You can also see this error if you have all the atoms but they're mis-named (according to Rosetta). The fix for that is to rename the atoms to the ones which Rosetta is expecting. You can do this manually, but there's also a `-remap_pdb_atom_names_for` option with Rosetta input, which gets passed the three letter code of the residue you want to try remapping. Note that the heuristic it uses to rename atoms is somewhat flakey, so my recommendation is not to use the flag routinely, but instead to pre-process the input file with it. (e.g. by using the score_jd2 application with the -out:pdb option), double check the renaming and then use the renamed file for your normal input.
But if your input file came out of a prior Rosetta run, there's no reason that a subsequent Rosetta run should have issues with the number or names of the atoms present -- presuming you used the same settings for PDB file reading (e.g. same scorefunction generation and same set of params files). If that's the case, you probably want to dig more into what's happening that you're getting the discrepancy.
I do want to include my ligand in protein A as a binary complex to dock to protein B.
So, my working pdb file includes three componets, protein A + ligand A is manually moved away from protein B but not too far for local docking. The ligand A's coordinate is from molfile_to_params.py step, which should be following Rosetta's naming rule.
PDB file: protein_B_protein_A_ligand.pdb (dont worry about the context shifting, I am sure it follows the pdb format)
...
ATOM 2452 HD13 LEU A 164 37.217 -20.566 23.886 1.00 92.14 H
ATOM 2453 HD21 LEU A 164 38.886 -20.203 26.270 1.00 91.90 H
ATOM 2454 HD22 LEU A 164 39.741 -20.604 24.813 1.00 91.90 H
ATOM 2455 HD23 LEU A 164 40.197 -19.212 25.772 1.00 91.90 H
ATOM 1 C1 LIG A 1 28.644 5.604 41.594 1.00 20.00 C
ATOM 2 C2 LIG A 1 23.659 -2.330 34.392 1.00 20.00 C
ATOM 3 C3 LIG A 1 22.395 -2.793 33.720 1.00 20.00 C
ATOM 4 C4 LIG A 1 21.346 -3.293 34.688 1.00 20.00 C
ATOM 5 C5 LIG A 1 21.173 -2.346 35.850 1.00 20.00 C
ATOM 6 C6 LIG A 1 20.349 -2.985 36.910 1.00 20.00 C
...
ATOM 70 H34 LIG A 1 25.960 3.836 39.464 1.00 20.00 H
ATOM 71 H35 LIG A 1 25.783 0.889 36.586 1.00 20.00 H
ATOM 72 H36 LIG A 1 22.392 -1.399 37.179 1.00 20.00 H
ATOM 73 H37 LIG A 1 17.523 0.978 35.322 1.00 20.00 H
ATOM 74 H38 LIG A 1 27.975 6.876 43.451 1.00 20.00 H
END
In my first run, I did not include "-extra_res_fa LIG.params" in my input, and it did generate poses, but missing atoms in the ligand part.
#######
-in:file:s input_files/protein_B_protein_A_ligand.pdb
-nstruct 1
-partners B_A
-dock_pert 3 8
-ex1
-ex2aro
-out:path:all output_files
-out:suffix _local_dock
-overwrite
#######
I my second run, I included "-extra_res_fa LIG.params" in my input, it did not generate any poses and showed error and calculation died.
#######
-in:file:s input_files/protein_B_protein_A_ligand.pdb
-extra_res_fa LIG.params
-nstruct 1
-partners B_A
-dock_pert 3 8
-ex1
-ex2aro
-out:path:all output_files
-out:suffix _local_dock
-overwrite
########
Your outputs from when you didn't provide the -extra_res_fa are junk.
Rosetta these days contains the PDB's Chemical Component Dictionary, such that it can attempt to read from-PDB structures natively. The CCD has a LIG entry, but it's probably not what you want. Note that when you provide a params file with -extra_res_fa, that definition with override the CCD's entry. (As we assume you know better what you want.)
So what happens when you don't provide the -extra_res_fa is that Rosetta attempts to read in your ligand as the CCD's LIG ligand. Any time you're working with a structure with that ligand, you need to specify the -extra_res_fa flag with your params file, as the params file is the only way Rosetta knows how the ligand behaves.
-----
That said, it sounds like you're not using the output from the no -extra_res_fa step for further processing. If I'm understanding correctly, you're using the PDB which is spit out by molfile_to_params.py as your input, and then running that PDB with the params file produced by that run. -- You're right, that should work, and I'm not sure why it isn't.
My suggestion would be to re-do the molfile_to_params.py step, and then redo your setup and runs using that fresh output, making sure that your PDB input and params files are coming from the same run of molfile_to_params.
If that doesn't work, then I'd probably have to debug the run locally (e.g. you post all the inputs I'd need to replicate the run here) in order to figure out what's going on.
Thanks for the reply.
You are right, LIG is not what I want, then what should I rename my ligand to a new one that CDD has not registered? Even my orginal RMC is registered in CDD with a different ligand.
I redid the ligand prep step by keeping my ligand' three letter node. I took the ligand's coord from my Protein A+ ligand A complex, and saved my ligand.pdb as ligand.sdf, then rerun the molfile_to_params.py to generate RMC.params and RMC.pdb. I then pasted the generated ligand coord to my ProteinA pdb to generate a working protein A+ lig A +protein B pdb. I also specified -extra_res_fa ligand_prep/RMC.params and with and without (-ignore_unrecognized_res) to bypass my ligand naming issue.
still, the following error poped out:
####
core.conformation.Residue: [ ERROR ] Cannot build coordinates for residue pdb_RMC at position 690: missing too many atoms.
core.conformation.Residue: [ ERROR ] Missing atoms are: OAP CAQ CAR CAK CAI NAS CAT NAU CAV NAW CAZ CAY CBA CAX CAN NAO NAL CAM NAJ CAD CAE CAG CAH CAF CAC CAB CBB HAP HAS
ERROR: Unable to fill in missing atoms.
ERROR:: Exit from: src/core/conformation/Residue.cc line: 1376
protocols.jd2.JobDistributor: [ ERROR ]
#####
Rosetta generated and naming my atom name as C1 C2 C3 H1 H2 ....H33 in the params and pdb anyway.
The residue names which start with "pdb_" are the chemical component dictionary ones. The fact that it's trying to use the pdb_RMC definition means that it's not using your params file.
I'm not sure why. If you supply a params file, it should override the CCD version. The fact that it isn't means that it either isn't reading your params file or your params file has an issue.
On the latter, double check the contents. You should have a `NAME RMC` line and an IO_STRING RMS z` line near the top. If RMC does not occur in either/both of your NAME/IO_STRING lines for your params file, that indicates that there might be something off about your params file.
If that's fine, it may be that Rosetta is not properly reading the params file. Take a look at the tracer output. In particular, check the output where it repeats the parameters passed to the command line - is the -extra_res_fa there? Also check later, to see if there's some mention of your params file. You might want to try adding the option `-out:levels core.chemical.GlobalResidueTypeSet:debug` to your command line, and then look for a message about loading the residue type RMC from the RMC.params file.
NAME RMC is there, IO_STRING RMS Z is also there in the RMC.params file.
Using the `-out:levels core.chemical.GlobalResidueTypeSet:debug` in the input file, it checked many residue type in the database, but nothing for RMC.
I do not find the "-extra_res_fa" in the output trace, but I see this:
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_DAB from file home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QR6.params
core.chemical.GlobalResidueTypeSet: initializing ResidueTypes from commandline
core.chemical.GlobalResidueTypeSet: Loading ResidueType RMC from file ligand_prep/RMC.params
core.chemical.GlobalResidueTypeSet: initializing patches from commandline
core.chemical.GlobalResidueTypeSet: initializing patches from database
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.6 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
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingInitialPerturbation: Reading options...
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input_files/b_catenin_trpa_rmc_1.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input_files/b_catenin_trpa_rmc_1.pdb
core.import_pose.import_pose: File 'input_files/b_catenin_trpa_rmc_1.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Not loading 'ALA' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'VAL' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'ASN' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'LEU' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'ILE' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'TYR' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'GLN' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'ASP' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'GLU' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'THR' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'ARG' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'PRO' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'LYS' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'MET' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'HIS' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'SER' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'CYS' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'GLY' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'PHE' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'TRP' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'RMC' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 235 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 369 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 659 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 673 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 683 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingInitialPerturbation: Reading options...
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor!
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 529 -1 EDGE 1 530 1 EDGE 530 711 -1 EDGE 1 712 2
protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 253 -1 EDGE 253 529 -1 EDGE 253 645 1 EDGE 645 530 -1 EDGE 645 711 -1 EDGE 711 712 2
protocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////
protocols.docking.DockingProtocol: /// Rosetta 3 Docking Protocol ///
protocols.docking.DockingProtocol: /// ///
protocols.docking.DockingProtocol: /// Dockable Jumps: 1 ///
protocols.docking.DockingProtocol: /// Low Resolution Docking Protocol: on ///
protocols.docking.DockingProtocol: /// High Resolution Docking Protocol: on ///
protocols.docking.DockingProtocol: /// Low Resolution Filter: on ///
protocols.docking.DockingProtocol: /// High Resolution Filter: on ///
protocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////
core.chemical.GlobalResidueTypeSet: Loading exclude_pdb_component PDB IDs from /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/exclude_pdb_component_list.txt
core.chemical.GlobalResidueTypeSet: initializing ResidueTypes from database
core.chemical.GlobalResidueTypeSet: Loading ResidueType ALA from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/ALA.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ARG from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/ARG.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ASN from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/ASN.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ASP from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/ASP.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType CYS from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/CYS.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType CYZ from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/CYZ.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType GLN from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/GLN.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType GLU from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/GLU.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType GLY from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/GLY.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType HIS from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/HIS.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType HIS_D from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/HIS_D.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ILE from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/ILE.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType LEU from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/LEU.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType LYS from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/LYS.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType MET from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/MET.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PHE from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/PHE.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRO from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/PRO.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType SER from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/SER.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType THR from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/THR.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType TRP from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/TRP.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType TYR from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/TYR.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType VAL from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-caa/VAL.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ORN from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-ncaa/ornithine.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType DPP from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-ncaa/2.3-diaminopropionic_acid.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType DAB from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/l-ncaa/2.4-diaminobutyric_acid.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType AIB from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/achiral_ncaa/AIB.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ADE from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/nucleic/dna/ADE.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType THY from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/nucleic/dna/THY.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType CYT from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/nucleic/dna/CYT.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType GUA from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/nucleic/dna/GUA.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType RAD from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/nucleic/rna_phenix/RAD_n.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType RCY from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/nucleic/rna_phenix/RCY_n.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType RGU from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/nucleic/rna_phenix/RGU_n.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType URA from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/nucleic/rna_phenix/URA_n.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ZN from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/metal_ions/ZN.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType MG from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/metal_ions/MG.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType CA from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/metal_ions/CA.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType VRT from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/rosetta_specific/VRT.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType INV_VRT from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/rosetta_specific/INV_VRT.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType STAPLE08A from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/staple/08A.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType STAPLE08B from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/staple/08B.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType EMB from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/membrane/EMB.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType MEM from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/centroid/residue_types/membrane/MEM.params
core.chemical.GlobalResidueTypeSet: initializing ResidueTypes from commandline
core.chemical.GlobalResidueTypeSet: initializing patches from commandline
core.chemical.GlobalResidueTypeSet: initializing patches from database
core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.01 seconds.
core.chemical.GlobalResidueTypeSet: Converting PDB component RMC to centroid.
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'RMC' from the PDB components dictionary for residue type 'pdb_RMC'
core.conformation.Residue: [ ERROR ] Cannot build coordinates for residue pdb_RMC at position 712: missing too many atoms.
core.conformation.Residue: [ ERROR ] Missing atoms are: OAP CAQ CAR CAK CAI NAS CAT NAU CAV NAW CAZ CAY CBA CAX CAN NAO NAL CAM NAJ CAD CAE CAG CAH CAF CAC CAB CBB HAP HAS
ERROR: Unable to fill in missing atoms.
ERROR:: Exit from: src/core/conformation/Residue.cc line: 1376
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job b_catenin_trpa_rmc_1_local_dock_0001
[ ERROR ]: Caught exception:
File: src/core/conformation/Residue.cc:1376
[ ERROR ] UtilityExitException
ERROR: Unable to fill in missing atoms.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: [ WARNING ] b_catenin_trpa_rmc_1_local_dock_0001 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 3 seconds
---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
My working pdb is too big to upload, but I uploaded the params (saved as .txt), and input flag for your reference.
This looks to be indicating the issue. The initial load of your RMC parameters is fine, but when you switch to centroid mode then things mess up and it goes to the CCD.
When you use molfile_to_params.py, there's a `--centroid` option you can pass to also output centroid-mode parameters. If you pass those parameters to Rosetta with the `-extra_res_cen` command line, then it should be able to use those parameters when it switches to centroid mode.
Thanks, I tried the "--centroid" to generate both the RMC.fa.params and RMC.cen.params. I aslo specified the "-extra_res_cen" in the input file. Some hydrogens were ignored in the RMC.cen.params and RMC.cen.pdb. Also, notice, RMC.cen_conformers.pdb and RMC.fa_conformers.pdb are empty.
######
-in:file:s input_files/b_catenin_trpa_rmc_1.pdb
-ignore_unrecognized_res
-in:file:extra_res_cen ligand_prep/RMC.cen.params
-nstruct 1
-partners B_A
-dock_pert 3 8
-ex1
-ex2aro
-out:path:all output_files
-out:suffix _local_dock
-out:levels core.chemical.GlobalResidueTypeSet:debug
-overwrite
##########
Here is what I had:
kwu@cs008:~/rosetta_3.13/main/demos/tutorials/Protein-Protein-Docking_1$ $ROSETTA/bin/docking_protocol.static.linuxgccrelease @flag_local_docking
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.linux.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:52:25.363712
core.init: command: /home/kwu/rosetta_3.13/main/source/bin/docking_protocol.static.linuxgccrelease @flag_local_docking
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-894855536 seed_offset=0 real_seed=-894855536
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-894855536 RG_type=mt19937
core.init: Resolved executable path: /home/kwu/rosetta_3.13/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/docking_protocol.static.linuxgccrelease
core.init: Looking for database based on location of executable: /home/kwu/rosetta_3.13/main/database/
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_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
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: Loading exclude_pdb_component PDB IDs from /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/exclude_pdb_component_list.txt
core.chemical.GlobalResidueTypeSet: initializing ResidueTypes from database
core.chemical.GlobalResidueTypeSet: Loading ResidueType ALA from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ALA.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ARG from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ARG.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ASN from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ASN.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType ASP from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ASP.params
...
pe_sets/fa_standard/residue_types/oligourea/OU3_ALA.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_ILE from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_ILE.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_LEU from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_LEU.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_PHE from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_PHE.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_ASN from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_ASN.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_PRO from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_PRO.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_THR from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_THR.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_GLN from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_GLN.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_VAL from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_VAL.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_TRP from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_TRP.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType OU3_TYR from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/oligourea/OU3_TYR.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType CA from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CA.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType CD from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CD.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType CO from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CO.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType CU from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CU.params
...
core.chemical.GlobalResidueTypeSet: Loading ResidueType C61 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-ncaa/trifluoro-leucine.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType TES from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-ncaa/TES.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType S56 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-ncaa/S56.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 001 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/001.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 003 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/003.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 004 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/004.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 005 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/005.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 006 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/006.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 007 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/007.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 009 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/009.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 010 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/010.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 020 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/020.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 101 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/101.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 102 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/102.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 103 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/103.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 104 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/104.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 111 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/111.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType 114 from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/peptoids/114.params
...
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_VAL from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QRV.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_TRP from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QRW.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_TYR from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QRY.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_FLUORO from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QR1.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_ETHYL from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QR2.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_PROPYL from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QR3.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_ORN from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QR4.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_DAP from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QR5.params
core.chemical.GlobalResidueTypeSet: Loading ResidueType PRE_METHYLENE_POST_METHYLENE_PARA_POLYARAMID_DAB from file /home/kwu/rosetta_3.13/main/database/chemical/residue_type_sets/fa_standard/residue_types/polyaramids/QR6.params
core.chemical.GlobalResidueTypeSet: initializing ResidueTypes from commandline
core.chemical.GlobalResidueTypeSet: initializing patches from commandline
core.chemical.GlobalResidueTypeSet: initializing patches from database
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 984 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.57 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
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingInitialPerturbation: Reading options...
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input_files/b_catenin_trpa_rmc_1.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input_files/b_catenin_trpa_rmc_1.pdb
core.import_pose.import_pose: File 'input_files/b_catenin_trpa_rmc_1.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Not loading 'ALA' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'VAL' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'ASN' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'LEU' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'ILE' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'TYR' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'GLN' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'ASP' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'GLU' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'THR' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'ARG' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'PRO' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'LYS' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'MET' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'HIS' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'SER' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'CYS' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'GLY' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'PHE' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Not loading 'TRP' from PDB components dictionary because it is in exclude_pdb_component_list.txt in the ResidueTypeSet.
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'RMC' from the PDB components dictionary for residue type 'pdb_RMC'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 235 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 369 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 659 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 673 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 683 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: HIS
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 90 atoms at position 712 in file input_files/b_catenin_trpa_rmc_1.pdb. Best match rsd_type: pdb_RMC
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'b_catenin_trpa_rmc_1_local_dock_0001'
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
[ ERROR ]: Caught exception:
File: src/core/id/NamedAtomID_Map.hh:390
Residue outside res_map range
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: b_catenin_trpa_rmc_1_local_dock_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 1 seconds
---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------
Docking has both fullatom and centroid stages, so you need to provide both full atom and centroid params files. `-extra_res_fa RMC.fa.params -extra_res_cen RMC.cen.params`
The "missing" hydrogens in the centroid params/PDB are expected. To save on computation, centroid mode uses a "united atom" model with nonpolar hydrogens, merging their properties into the atom type of the attached heavyatom.
Thank you! It seems reading both the .fa.params and .cen.params files.
But here imposes another error:
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /shared/rosetta_bin_linux_2021.16.61629_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/shared/rosetta_bin_linux_2021.16.61629_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.16 seconds to load from binary
ERROR: PDB Rotamers file 'ligand_prep/RMC.fa_conformers.pdb' does not contain any usable rotamers!.
ERROR:: Exit from: src/core/pack/rotamers/SingleLigandRotamerLibrary.cc line: 113
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job protein_0011_local_dock_0001
[ ERROR ]: Caught exception:
File: src/core/pack/rotamers/SingleLigandRotamerLibrary.cc:113
[ ERROR ] UtilityExitException
ERROR: PDB Rotamers file 'ligand_prep/RMC.fa_conformers.pdb' does not contain any usable rotamers!.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: [ WARNING ] protein_0011_local_dock_0001 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 10 seconds
---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
Note: I got two "empty" fa_conformers.pdb and cen_conformers.pdb files, I am not sure why I got no rotamers during the ligand prep step. I only have one ligand comformation as input
-rw-r--r-- 1 kwu domain users 0 May 17 22:59 RMC.cen_conformers.pdb
-rw-r--r-- 1 kwu domain users 5909 May 17 22:59 RMC.cen.params
-rw-r--r-- 1 kwu domain users 3402 May 17 22:59 RMC.cen.pdb
-rw-r--r-- 1 kwu domain users 0 May 17 22:59 RMC.fa_conformers.pdb
-rw-r--r-- 1 kwu domain users 10066 May 17 22:59 RMC.fa.params
-rw-r--r-- 1 kwu domain users 6075 May 17 22:59 RMC.fa.pdb
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Below is the input:
-in:file:s input_files/protein_0011.pdb
-in:file:extra_res_fa ligand_prep/RMC.fa.params
-in:file:extra_res_cen ligand_prep/RMC.cen.params
-nstruct 1
-partners B_A
-dock_pert 3 8
-ex1
-ex2aro
-out:path:all output_files
-out:suffix _local_dock
-overwrite
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If you don't have any conformers in the rotamer file (if it's blank), just edit the params file and remove the PDB_ROTAMERS line. (That line is optional.)
Thank you so much! Prof. Moretti.
Everything works out!