Galaxy | BIOBB | Published Workflow | AMBER Protein Ligand Complex MD Setup

AMBER Protein Ligand Complex MD Setup

Annotation:

Step	Annotation
Step 1: Pdb output PDB name mypdb.pdb Take tool settings: Manual Input Properties Input: pdb_code 3htb filter Empty. api_id pdbe - PDB in Europe REST API
Step 2: RemovePdbWater input PDB file Output dataset 'output_pdb_path' from step 1 output PDB name myremove_pdb_water.pdb Take tool settings: Manual Input Properties Input: binary_path check_structure
Step 3: RemoveLigand input PDB,GRO file Output dataset 'output_pdb_path' from step 2 output PDB,GRO name myremove_ligand.pdb Take tool settings: Manual Input Properties Input: ligand PO4 output_format pdb
Step 4: RemoveLigand input PDB,GRO file Output dataset 'output_structure_path' from step 3 output PDB,GRO name myremove_ligand.pdb Take tool settings: Manual Input Properties Input: ligand BME output_format pdb
Step 5: Pdb4amberRun input PDB file Output dataset 'output_structure_path' from step 4 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 6: ExtractHeteroatoms input PDB,PDBQT file Output dataset 'output_pdb_path' from step 5 output PDB,PDBQT name myextract_heteroatoms.pdb Take tool settings: Manual Input Properties Input: heteroatoms [{"name": "JZ4"}] water False output_format pdb
Step 7: ReduceAddHydrogens input PDB file Output dataset 'output_heteroatom_path' from step 6 output PDB name myreduce_add_hydrogens.pdb Take tool settings: Manual Input Properties Input: flip False noflip False nuclear True nooh False oh True his False noheth False rotnh3 True norotnh3 False rotexist False rotexoh False allalt True onlya False charges False dorotmet False noadjust False metal_bump 0.0 non_metal_bump 0.0 build False binary_path reduce
Step 8: BabelMinimize input PDB,MOL2 file Output dataset 'output_path' from step 7 output PDB,MOL2 name mybabel_minimize.mol2 Take tool settings: Manual Input Properties Input: criteria 1e-10 method sd - steepest descent algorithm force_field GAFF - General Amber Force Field hydrogens False steps 2500 cutoff False rvdw 6.0 rele 10.0 frequency 10 binary_path obminimize output_format pdb
Step 9: AcpypeParamsAc input PDB,MDL,MOL2 file Output dataset 'output_path' from step 8 output FRCMOD name myacpype_params_ac.frcmod output INPCRD name myacpype_params_ac.inpcrd output LIB name myacpype_params_ac.lib output PRMTOP name myacpype_params_ac.prmtop Take tool settings: Manual Input Properties Input: basename JZ4params charge 0 binary_path acpype
Step 10: LeapGenTop input PDB file Output dataset 'output_pdb_path' from step 5 input LIB,ZIP file Output dataset 'output_path_lib' from step 9 input FRCMOD,ZIP file Output dataset 'output_path_frcmod' from step 9 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 gaff 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": 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 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 {"maxcyc": 500, "ntpr": 5, "ntr": 1, "restraintmask": "\":JZ4\"", "restraint_wt": 500.0} 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 14: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 13 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 15: AmberToPdb input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 10 input CRD,MDCRD,INPCRD,RST file Output dataset 'output_rst_path' from step 13 output PDB name myamber_to_pdb.pdb Take tool settings: Manual Input Properties Input: binary_path ambpdb
Step 16: LeapSolvate input PDB file Output dataset 'output_pdb_path' from step 15 input LIB,ZIP file Output dataset 'output_path_lib' from step 9 input FRCMOD,ZIP file Output dataset 'output_path_frcmod' from step 9 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.parmtop output CRD,MDCRD,INPCRD name myleap_solvate.crd Take tool settings: Manual Input Properties Input: forcefield protein.ff14SB gaff 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 17: LeapAddIons input PDB file Output dataset 'output_pdb_path' from step 16 input LIB,ZIP file Output dataset 'output_path_lib' from step 9 input FRCMOD,ZIP file Output dataset 'output_path_frcmod' from step 9 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.parmtop output CRD,MDCRD,INPCRD name myleap_add_ions.crd Take tool settings: Manual Input Properties Input: forcefield protein.ff14SB gaff 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 18: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 17 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_crd_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 Output dataset 'output_crd_path' from step 17 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": 15.0} 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 19: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 18 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 20: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 17 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 18 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 18 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, "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 21: ProcessMdout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 20 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 22: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 17 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 20 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 20 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": 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 23: ProcessMdout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 22 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 24: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 17 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 22 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 22 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": 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 25: ProcessMdout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 24 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 26: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 17 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 24 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 27: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_top_path' from step 17 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 26 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 28: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_top_path' from step 17 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 26 input PDB file Output dataset 'output_pdb_path' from step 10 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 29: CpptrajRgyr input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_top_path' from step 17 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 26 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 30: CpptrajImage input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_top_path' from step 17 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 26 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 Ligand Complex MD Setup

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