Galaxy | BIOBB | Published Workflow | AMBER Protein MD Setup

AMBER Protein MD Setup

Annotation:

Step	Annotation
Step 1: Pdb output PDB name mypdb.pdb Take tool settings: Manual Input Properties Input: pdb_code 1AKI filter [ATOM, MODEL, ENDMDL] api_id pdbe - PDB in Europe REST API
Step 2: Pdb4amberRun input PDB file Output dataset 'output_pdb_path' from step 1 output PDB name mypdb4amber_run.pdb Take tool settings: Manual Input Properties Input: remove_hydrogens False remove_waters False constant_pH False binary_path pdb4amber
Step 3: LeapGenTop input PDB file Output dataset 'output_pdb_path' from step 2 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 4: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 3 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_crd_path' from step 3 input MDIN,IN,TXT file select at runtime input CPIN file select at runtime input RST,RST7,NETCDF,NC,NCRST,CRD file Output dataset 'output_crd_path' from step 3 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.x 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 {"maxcyc": 500, "ntpr": 5, "ntr": 1, "restraintmask": "\":*&!@H=\"", "restraint_wt": 50.0} simulation_type min_vacuo - Runs an energy minimization in vacuo 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 5: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 3 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 4 input MDIN,IN,TXT file select at runtime input CPIN file select at runtime input RST,RST7,NETCDF,NC,NCRST,CRD file Output dataset 'output_rst_path' from step 4 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.x 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 {"maxcyc": 500, "ntpr": 5, "ntr": 1, "restraintmask": "\":*&!@H=\"", "restraint_wt": 50.0} simulation_type min_vacuo - Runs an energy minimization in vacuo 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 6: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 4 output DAT,TXT,CSV name myprocess_minout.dat Take tool settings: Manual Input Properties Input: terms ENERGY binary_path process_minout.perl output_format dat
Step 7: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 5 output DAT,TXT,CSV name myprocess_minout.dat Take tool settings: Manual Input Properties Input: terms ENERGY binary_path process_minout.perl output_format dat
Step 8: AmberToPdb input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 3 input CRD,MDCRD,INPCRD,RST file Output dataset 'output_rst_path' from step 5 output PDB name myamber_to_pdb.pdb Take tool settings: Manual Input Properties Input: binary_path ambpdb
Step 9: LeapSolvate input PDB file Output dataset 'output_pdb_path' from step 8 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_solvate.pdb output TOP,PARMTOP,PRMTOP name myleap_solvate.top output CRD,MDCRD,INPCRD name myleap_solvate.crd Take tool settings: Manual Input Properties Input: forcefield protein.ff14SB water_type TIP3PBOX box_type truncated_octahedron ions_type ionsjc_tip3p neutralise False iso False positive_ions_number 0 negative_ions_number 0 positive_ions_type Na+ negative_ions_type Cl- distance_to_molecule 9.0 closeness 1.0 binary_path tleap output_top_path_format top output_crd_path_format crd
Step 10: LeapAddIons input PDB file Output dataset 'output_pdb_path' from step 9 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_add_ions.pdb output TOP,PARMTOP,PRMTOP name myleap_add_ions.top output CRD,MDCRD,INPCRD name myleap_add_ions.crd Take tool settings: Manual Input Properties Input: forcefield protein.ff14SB water_type TIP3PBOX box_type truncated_octahedron ions_type ionsjc_tip3p neutralise True ionic_concentration 150.0 positive_ions_number 0 negative_ions_number 0 positive_ions_type Na+ negative_ions_type Cl- binary_path tleap output_top_path_format top output_crd_path_format crd
Step 11: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 10 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_crd_path' from step 10 input MDIN,IN,TXT file select at runtime input CPIN file select at runtime input RST,RST7,NETCDF,NC,NCRST,CRD file Output dataset 'output_crd_path' from step 10 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.x 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 {"maxcyc": 300, "ntr": 1, "restraintmask": "\"!:WAT,Cl-,Na+\"", "restraint_wt": 50.0} 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 12: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 11 output DAT,TXT,CSV name myprocess_minout.dat Take tool settings: Manual Input Properties Input: terms ENERGY binary_path process_minout.perl output_format dat
Step 13: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 10 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 11 input MDIN,IN,TXT file select at runtime input CPIN file select at runtime input RST,RST7,NETCDF,NC,NCRST,CRD file Output dataset 'output_rst_path' from step 11 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.x 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 {"nstlim": 2500, "ntr": 1, "restraintmask": "\"!:WAT,Cl-,Na+\"", "restraint_wt": 10.0} simulation_type heat - Heats the MD system 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 14: ProcessMdout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 13 output DAT,TXT,CSV name myprocess_mdout.dat Take tool settings: Manual Input Properties Input: terms TEMP binary_path process_mdout.perl output_format dat
Step 15: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 10 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 13 input MDIN,IN,TXT file select at runtime input CPIN file select at runtime input RST,RST7,NETCDF,NC,NCRST,CRD file Output dataset 'output_rst_path' from step 13 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.x 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 {"nstlim": 500, "ntr": 1, "restraintmask": "\"!:WAT,Cl-,Na+ & !@H=\"", "restraint_wt": 5.0} simulation_type NVT - Runs an NVT equilibration 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 16: ProcessMdout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 15 output DAT,TXT,CSV name myprocess_mdout.dat Take tool settings: Manual Input Properties Input: terms TEMP binary_path process_mdout.perl output_format dat
Step 17: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 10 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 15 input MDIN,IN,TXT file select at runtime input CPIN file select at runtime input RST,RST7,NETCDF,NC,NCRST,CRD file Output dataset 'output_rst_path' from step 15 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.x 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 {"nstlim": 500, "ntr": 1, "restraintmask": "\"!:WAT,Cl-,Na+ & !@H=\"", "restraint_wt": 2.5} simulation_type npt - Runs an NPT equilibration 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: ProcessMdout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 17 output DAT,TXT,CSV name myprocess_mdout.dat Take tool settings: Manual Input Properties Input: terms PRES DENSITY binary_path process_mdout.perl output_format dat
Step 19: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 10 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 17 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.netcdf 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 {"nstlim": 2500, "ntwx": 500} simulation_type free - Runs a MD simulation 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 20: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_top_path' from step 10 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_traj_path' from step 19 input PDB file select at runtime output DAT,AGR,XMGR,GNU name mycpptraj_rms.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 mycpptraj_rms.mdcrd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask backbone - Backbone atoms reference first - Use the first trajectory frame as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format mdcrd
Step 21: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_top_path' from step 10 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_traj_path' from step 19 input PDB file Output dataset 'output_pdb_path' from step 1 output DAT,AGR,XMGR,GNU name mycpptraj_rms.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 mycpptraj_rms.mdcrd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask backbone - Backbone atoms 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 mdcrd
Step 22: CpptrajRgyr input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_top_path' from step 10 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_traj_path' from step 19 output DAT,AGR,XMGR,GNU name mycpptraj_rgyr.dat Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask backbone - Backbone atoms binary_path cpptraj output_format dat
Step 23: CpptrajImage input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_top_path' from step 10 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_traj_path' from step 19 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_image.trr Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask solute - All system atoms except solvent atoms format trr - Trajectory of a simulation experiment used by GROMACS binary_path cpptraj output_format mdcrd

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AMBER Protein MD Setup

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