Galaxy | BIOBB | Published Workflow | Macromolecular Coarse-Grained Flexibility

Macromolecular Coarse-Grained Flexibility

Annotation:

Step	Annotation
Step 1: Pdb output PDB name mypdb.pdb Take tool settings: Manual Input Properties Input: pdb_code 1a32 filter Empty. api_id pdbe - PDB in Europe REST API
Step 2: ExtractAtoms input PDB,GRO file Output dataset 'output_pdb_path' from step 1 output PDB,GRO name structure_ca.pdb Take tool settings: Manual Input Properties Input: regular_expression_pattern ^CA output_format pdb
Step 3: NmaRun input PDB file Output dataset 'output_structure_path' from step 2 output LOG,OUT,TXT,O name nma_ensemble.log output CRD,MDCRD,INPCRD name nma_ensemble.mdcrd Take tool settings: Manual Input Properties Input: binary_path diaghess frames 50 nvecs 50 output_log_path_format log output_crd_path_format crd
Step 4: DmdRun input PDB file Output dataset 'output_structure_path' from step 2 output LOG,OUT,TXT,O name dmd_ensemble.log output CRD,MDCRD,INPCRD name dmd_ensemble.mdcrd Take tool settings: Manual Input Properties Input: binary_path dmdgoopt dt 1e-12 temperature 300 frames 1000 output_log_path_format log output_crd_path_format crd
Step 5: BdRun input PDB file Output dataset 'output_structure_path' from step 2 output LOG,OUT,TXT,O name bd_ensemble.log output CRD,MDCRD,INPCRD name bd_ensemble.mdcrd Take tool settings: Manual Input Properties Input: binary_path bd time 10000 dt 1e-15 wfreq 100 output_log_path_format log output_crd_path_format crd
Step 6: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 2 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 3 input PDB file Output dataset 'output_structure_path' from step 2 output DAT,AGR,XMGR,GNU name nma_ensemble_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name nma_ensemble.dcd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format dcd
Step 7: PczZip input PDB file Output dataset 'output_structure_path' from step 2 input CRD,MDCRD,INPCRD file Output dataset 'output_crd_path' from step 3 output PCZ name nma_ensemble.pcz Take tool settings: Manual Input Properties Input: binary_path pcazip neigenv 10 variance 90 verbose False gauss_rmsd True
Step 8: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 2 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 4 input PDB file Output dataset 'output_structure_path' from step 2 output DAT,AGR,XMGR,GNU name dmd_ensemble_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name dmd_ensemble.dcd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format dcd
Step 9: PczZip input PDB file Output dataset 'output_structure_path' from step 2 input CRD,MDCRD,INPCRD file Output dataset 'output_crd_path' from step 4 output PCZ name dmd_ensemble.pcz Take tool settings: Manual Input Properties Input: binary_path pcazip neigenv 10 variance 90 verbose False gauss_rmsd True
Step 10: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 2 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 5 input PDB file Output dataset 'output_structure_path' from step 2 output DAT,AGR,XMGR,GNU name bd_ensemble_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name bd_ensemble.dcd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format dcd
Step 11: PczZip input PDB file Output dataset 'output_structure_path' from step 2 input CRD,MDCRD,INPCRD file Output dataset 'output_crd_path' from step 5 output PCZ name bd_ensemble.pcz Take tool settings: Manual Input Properties Input: binary_path pcazip neigenv 10 variance 90 verbose False gauss_rmsd True
Step 12: PczUnzip input PCZ file Output dataset 'output_pcz_path' from step 7 output CRD,MDCRD,INPCRD,PDB name nma_ensemble_uncompressed.crd Take tool settings: Manual Input Properties Input: binary_path pcaunzip verbose False pdb False output_format crd
Step 13: PczBfactor input PCZ file Output dataset 'output_pcz_path' from step 7 output DAT,TXT,CSV name bfactor_all.dat output PDB name bfactor_all.pdb Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 pdb True output_format dat
Step 14: PczAnimate input PCZ file Output dataset 'output_pcz_path' from step 7 output CRD,MDCRD,INPCRD,PDB name pcz_proj1.crd Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 1 pdb False output_format crd
Step 15: PczInfo input PCZ file Output dataset 'output_pcz_path' from step 7 output JSON name pcz_report.json Take tool settings: Manual Input Properties Input: binary_path pczdump
Step 16: PczEvecs input PCZ file Output dataset 'output_pcz_path' from step 7 output JSON name pcz_evecs.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 1
Step 17: PczStiffness input PCZ file Output dataset 'output_pcz_path' from step 7 output JSON name pcz_stiffness.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 temperature 300
Step 18: PczCollectivity input PCZ file Output dataset 'output_pcz_path' from step 7 output JSON name pcz_collectivity.json Take tool settings: Manual Input Properties Input: eigenvector 0 binary_path pczdump
Step 19: PczUnzip input PCZ file Output dataset 'output_pcz_path' from step 9 output CRD,MDCRD,INPCRD,PDB name dmd_ensemble_uncompressed.crd Take tool settings: Manual Input Properties Input: binary_path pcaunzip verbose False pdb False output_format crd
Step 20: PczUnzip input PCZ file Output dataset 'output_pcz_path' from step 11 output CRD,MDCRD,INPCRD,PDB name bd_ensemble_uncompressed.crd Take tool settings: Manual Input Properties Input: binary_path pcaunzip verbose False pdb False output_format crd
Step 21: PczHinges input PCZ file Output dataset 'output_pcz_path' from step 11 output JSON name hinges_dyndom_report.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 method Dynamic_domain
Step 22: PczHinges input PCZ file Output dataset 'output_pcz_path' from step 11 output JSON name hinges_bfactor_report.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 method Bfactor_slope
Step 23: PczHinges input PCZ file Output dataset 'output_pcz_path' from step 11 output JSON name hinges_fcte_report.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 method Force_constant
Step 24: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 2 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 12 input PDB file Output dataset 'output_structure_path' from step 2 output DAT,AGR,XMGR,GNU name nma_ensemble_uncompressed.rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name nma_ensemble_uncompressed.dcd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format dcd
Step 25: CpptrajConvert input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 2 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 14 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name pcz_proj1.dcd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only format dcd - AMBER trajectory format binary_path cpptraj output_format dcd
Step 26: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 2 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 19 input PDB file Output dataset 'output_structure_path' from step 2 output DAT,AGR,XMGR,GNU name dmd_ensemble_uncompressed.rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name dmd_ensemble_uncompressed.dcd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format dcd
Step 27: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 2 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 20 input PDB file Output dataset 'output_structure_path' from step 2 output DAT,AGR,XMGR,GNU name bd_ensemble_uncompressed.rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name bd_ensemble_uncompressed.dcd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format dcd

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Macromolecular Coarse-Grained Flexibility

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