Hi , I'm beginner to Rosetta . In ligand_docking , it is said "chain_id F does not exist" . There are two ligands and one receport to dock , I can not define chain F or chain X (in my dock.xml). I can not undersstand some answers about this question. I wish receive the answer.
the process in ligand_docking:
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: Added mover "transform_F"
protocols.rosetta_scripts.ParsedProtocol: Added mover "transform_X"
protocols.rosetta_scripts.ParsedProtocol: Added mover "high_res_docker_F"
protocols.rosetta_scripts.ParsedProtocol: Added mover "high_res_docker_X"
protocols.rosetta_scripts.ParsedProtocol: Added mover "final_F"
protocols.rosetta_scripts.ParsedProtocol: Added mover "final_X"
protocols.rosetta_scripts.ParsedProtocol: Added mover "add_scores_F"
protocols.rosetta_scripts.ParsedProtocol: Added mover "add_scores_X"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy FSR2_A.pdb kae_0001.pdb SAM_0001.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Transform - transform_F=======================
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id F does not exist
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job FSR2_A_kae_0001_SAM_0001_0001
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id F does not exist
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: [ WARNING ] FSR2_A_kae_0001_SAM_0001_0001 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy FSR2_A.pdb kae_0001.pdb SAM_0001.pdb
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy FSR2_A.pdb kae_0001.pdb SAM_0001.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Transform - transform_F=======================
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id F does not exist
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job FSR2_A_kae_0001_SAM_0001_0002
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id F does not exist
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: [ WARNING ] FSR2_A_kae_0001_SAM_0001_0002 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy FSR2_A.pdb kae_0001.pdb SAM_0001.pdb
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy FSR2_A.pdb kae_0001.pdb SAM_0001.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Transform - transform_F=======================
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id F does not exist
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job FSR2_A_kae_0001_SAM_0001_0003
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id F does not exist
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
protocols.jd2.JobDistributor: [ WARNING ] FSR2_A_kae_0001_SAM_0001_0003 reported failure and will NOT retry
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy FSR2_A.pdb kae_0001.pdb SAM_0001.pdb
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy FSR2_A.pdb kae_0001.pdb SAM_0001.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Transform - transform_F=======================
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:
File: src/core/pose/chains_util.cc:453
chain_id F does not exist
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job FSR2_A_kae_0001_SAM_0001_0004
[ ERROR ]: Caught exception:
File: src/core/pose/chains_util.cc:453
chain_id F does not exist
dock.xml :
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep"> </ScoreFunction>
<ScoreFunction name="hard_rep" weights="ligand"> </ScoreFunction>
</SCOREFXNS>
<LIGAND_AREAS>
<LigandArea name="inhibitor_dock_sc_F" chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
<LigandArea name="inhibitor_final_sc_F" chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
<LigandArea name="inhibitor_final_bb_F" chain="F" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
<LigandArea name="inhibitor_dock_sc_X" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
<LigandArea name="inhibitor_final_sc_X" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
<LigandArea name="inhibitor_final_bb_X" chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<InterfaceBuilder name="side_chain_for_docking_F" ligand_areas="inhibitor_dock_sc_F"/>
<InterfaceBuilder name="side_chain_for_final_F" ligand_areas="inhibitor_final_sc_F"/>
<InterfaceBuilder name="backbone_F" ligand_areas="inhibitor_final_bb_F" extension_window="3"/>
<InterfaceBuilder name="side_chain_for_docking_X" ligand_areas="inhibitor_dock_sc_X"/>
<InterfaceBuilder name="side_chain_for_final_X" ligand_areas="inhibitor_final_sc_X"/>
<InterfaceBuilder name="backbone_X" ligand_areas="inhibitor_final_bb_X" extension_window="3"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<MoveMapBuilder name="docking_F" sc_interface="side_chain_for_docking_F"/>
<MoveMapBuilder name="final_F" sc_interface="side_chain_for_final_F" bb_interface="backbone_F"/>
<MoveMapBuilder name="docking_X" sc_interface="side_chain_for_docking_X"/>
<MoveMapBuilder name="final_X" sc_interface="side_chain_for_final_X" bb_interface="backbone_X"/>
</MOVEMAP_BUILDERS>
<SCORINGGRIDS ligand_chain="F" width="15">
<ClassicGrid grid_name="classic" weight="1.0"/>
</SCORINGGRIDS>
<MOVERS>
<Transform name="transform_F" chain="F" box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="5"/>
<Transform name="transform_X" chain="X" box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="5"/>
<HighResDocker name="high_res_docker_F" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking_F"/>
<HighResDocker name="high_res_docker_X" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking_X"/>
<FinalMinimizer name="final_F" scorefxn="hard_rep" movemap_builder="final_F"/>
<FinalMinimizer name="final_X" scorefxn="hard_rep" movemap_builder="final_X"/>
<InterfaceScoreCalculator name="add_scores_F" chains="F" scorefxn="hard_rep"/>
<InterfaceScoreCalculator name="add_scores_X" chains="X" scorefxn="hard_rep"/>
</MOVERS>
<PROTOCOLS>
<Add mover_name="transform_F"/>
<Add mover_name="transform_X"/>
<Add mover_name="high_res_docker_F"/>
<Add mover_name="high_res_docker_X"/>
<Add mover_name="final_F"/>
<Add mover_name="final_X"/>
<Add mover_name="add_scores_F"/>
<Add mover_name="add_scores_X"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
options:
#Pound signs indicate comments
#-in:file:s option imports the protein and ligand PDB structures
#-in:file:extra_res_fa option imports the parameters for the ligand
-in
-file
-s "FSR2_A.pdb kae_0001.pdb SAM_0001.pdb"
-extra_res_fa sam.params
-extra_res_fa kae.params
#the packing options allow Rosetta to sample additional rotamers for
#protein sidechain angles chi 1 (ex1) and chi 2 (ex2)
#no_optH false tells Rosetta to optimize hydrogen placements
#flip_HNQ tells Rosetta to consider HIS,ASN,GLN hydrogen flips
#ignore_ligand_chi prevents Roseta from adding additional ligand rotamer
-packing
-ex1
-ex2
-no_optH false
-flip_HNQ true
-ignore_ligand_chi true
#parser:protocol locates the XML file for RosettaScripts
-parser
-protocol dock_two_sub_tras.xml
#overwrite allows Rosetta to write over previous structures and scores
-overwrite
#Ligand docking is not yet benchmarked with the updated scoring function
#This flag restores certain parameters to previously published values
-mistakes
-restore_pre_talaris_2013_behavior true
-nstruct 5
That error message means that your input PDB doesn't have the proper chain F.
The way you do in the input (-s "FSR2_A.pdb kae_0001.pdb SAM_0001.pdb") should work to concatenate all those structures. My initial guess would be that you don't have your "F" ligand properly annotated in the input file. I'm not sure if it's kae or SAM which you want to be "F", but I'd double check those PDBs to see what chain letters they're using. I'm guessing that the files you're using still have both ligands listed as chain X, and you'll simply need to edit the files (e.g. with a text editor) to change what the chain letter is.
Hi rmoretti, I edit chain F in the inputs (-s complex1.pdb) , the first step is ligand sam and receptor , the second step is ligand kae and receptor 2(complex1.pdb). This is success . I do not know it will effects the interaction between ligand-sam and ligand-kae . I found the location of ligand is not ture , "cat FSR2_A.pdb SAM_0001.pdb kae_0001.pdb > fsr2_SAM_kae.pdb" the location of ligand do not change . I'm not ture which step was false. Thank you for answering .