Galaxy | BIOBB | Published Workflow | Molecular Structure Checking

Molecular Structure Checking

Annotation:

Step	Annotation
Step 1: Pdb output PDB name mypdb.pdb Take tool settings: Manual Input Properties Input: pdb_code 1z83 filter [ATOM, HETATM] api_id pdbe - PDB in Europe REST API
Step 2: CanonicalFasta output FASTA name mycanonical_fasta.fasta Take tool settings: Manual Input Properties Input: pdb_code 1z83 api_id pdb - RCSB PDB REST API
Step 3: StructureCheck input PDB,PDBQT file Output dataset 'output_pdb_path' from step 1 output JSON name mystructure_check.json Take tool settings: Manual Input Properties Input: features Nothing selected. binary_path check_structure
Step 4: ExtractModel input PDB,PDBQT file Output dataset 'output_pdb_path' from step 1 output PDB,PDBQT name myextract_model.pdb Take tool settings: Manual Input Properties Input: models [1] binary_path check_structure output_format pdb
Step 5: ExtractChain input PDB,PDBQT file Output dataset 'output_structure_path' from step 4 output PDB,PDBQT name myextract_chain.pdb Take tool settings: Manual Input Properties Input: chains ["A"] permissive False binary_path check_structure output_format pdb
Step 6: FixAltlocs input PDB file Output dataset 'output_structure_path' from step 5 output PDB name myfix_altlocs.pdb Take tool settings: Manual Input Properties Input: altlocs ["A45:A", "A67:A", "A85:A"] modeller_key Empty. binary_path check_structure
Step 7: FixSsbonds input PDB file Output dataset 'output_pdb_path' from step 6 output PDB name myfix_ssbonds.pdb Take tool settings: Manual Input Properties Input: modeller_key Empty. binary_path check_structure
Step 8: RemoveMolecules input PDB,PDBQT file Output dataset 'output_pdb_path' from step 7 output PDB,PDBQT name myremove_molecules.pdb Take tool settings: Manual Input Properties Input: molecules [{"name": "ZN"}] output_format pdb
Step 9: RemoveMolecules input PDB,PDBQT file Output dataset 'output_molecules_path' from step 8 output PDB,PDBQT name myremove_molecules.pdb Take tool settings: Manual Input Properties Input: molecules [{"name": "SO4"}, {"name": "AP5"}] output_format pdb
Step 10: ReduceRemoveHydrogens input PDB file Output dataset 'output_molecules_path' from step 9 output PDB name myreduce_remove_hydrogens.pdb Take tool settings: Manual Input Properties Input: binary_path reduce
Step 11: RemovePdbWater input PDB file Output dataset 'output_path' from step 10 output PDB name myremove_pdb_water.pdb Take tool settings: Manual Input Properties Input: binary_path check_structure
Step 12: FixAmides input PDB file Output dataset 'output_pdb_path' from step 11 output PDB name myfix_amides.pdb Take tool settings: Manual Input Properties Input: modeller_key Empty. binary_path check_structure
Step 13: FixChirality input PDB file Output dataset 'output_pdb_path' from step 12 output PDB name myfix_chirality.pdb Take tool settings: Manual Input Properties Input: modeller_key Empty. binary_path check_structure
Step 14: FixSideChain input PDB file Output dataset 'output_pdb_path' from step 13 output PDB name myfix_side_chain.pdb Take tool settings: Manual Input Properties Input: use_modeller False modeller_key Empty. binary_path check_structure
Step 15: FixBackbone input PDB file Output dataset 'output_pdb_path' from step 14 input FASTA file Output dataset 'output_fasta_path' from step 2 output PDB name myfix_backbone.pdb Take tool settings: Manual Input Properties Input: add_caps False modeller_key MODELIRANJE binary_path check_structure
Step 16: LeapGenTop input PDB file Output dataset 'output_pdb_path' from step 15 input LIB,ZIP file select at runtime input FRCMOD,ZIP file select at runtime input IN,LEAPIN,TXT,ZIP file select at runtime input IN,LEAPIN,TXT,ZIP file select at runtime output PDB name myleap_gen_top.pdb output TOP,PARMTOP,PRMTOP name myleap_gen_top.top output CRD,MDCRD,INPCRD name myleap_gen_top.crd Take tool settings: Manual Input Properties Input: forcefield protein.ff14SB binary_path tleap output_top_path_format top output_crd_path_format crd
Step 17: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 16 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_crd_path' from step 16 input MDIN,IN,TXT file select at runtime input CPIN file select at runtime input RST,RST7,NETCDF,NC,NCRST,CRD file select at runtime output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.crd output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.rst output CPOUT name mysander_mdrun.cpout output CPRST,RST,RST7 name mysander_mdrun.cprst output MDINFO name mysander_mdrun.mdinfo Take tool settings: Manual Input Properties Input: mdin {"ntb":0,"cut":12,"maxcyc":500,"ncyc":50,"ntwx":50} simulation_type minimization - Runs an energy minimization binary_path sander mpi_bin Empty. mpi_np 0 mpi_flags Empty. output_log_path_format log output_traj_path_format trj output_rst_path_format rst output_cprst_path_format cprst
Step 18: AmberToPdb input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 16 input CRD,MDCRD,INPCRD,RST file Output dataset 'output_rst_path' from step 17 output PDB name myamber_to_pdb.pdb Take tool settings: Manual Input Properties Input: binary_path ambpdb
Step 19: StructureCheck input PDB,PDBQT file Output dataset 'output_pdb_path' from step 18 output JSON name mystructure_check.json Take tool settings: Manual Input Properties Input: features Nothing selected. binary_path check_structure

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gbayarri

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