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ABCix MD Setup

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Step	Annotation
Step 1: LeapGenTop input PDB file select at runtime 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 DNA.bsc1 binary_path tleap output_top_path_format top output_crd_path_format crd
Step 2: LeapSolvate input PDB file Output dataset 'output_pdb_path' from step 1 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.parmtop output CRD,MDCRD,INPCRD name myleap_solvate.crd Take tool settings: Manual Input Properties Input: forcefield DNA.bsc1 water_type OPCBOX box_type truncated_octahedron ions_type ionsjc_tip4pew neutralise True iso True positive_ions_number 0 negative_ions_number 0 positive_ions_type K+ negative_ions_type Cl- distance_to_molecule 15.0 closeness 0.97 binary_path tleap output_top_path_format parmtop output_crd_path_format crd
Step 3: LeapAddIons 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_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 DNA.bsc1 water_type OPCBOX box_type truncated_octahedron ions_type ionsjc_tip4pew neutralise True ionic_concentration 100.0 positive_ions_number 0 negative_ions_number 0 positive_ions_type K+ negative_ions_type Cl- binary_path tleap output_top_path_format top output_crd_path_format crd
Step 4: ParmedHmassrepartition input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 3 output TOP,PARMTOP,PRMTOP name myparmed_hmassrepartition.top Take tool settings: Manual Input Properties Input: binary_path parmed output_format top
Step 5: CpptrajRandomizeIons input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 3 input CRD,MDCRD,INPCRD file Output dataset 'output_crd_path' from step 3 output PDB name mycpptraj_randomize_ions.pdb output CRD,MDCRD,INPCRD name mycpptraj_randomize_ions.crd Take tool settings: Manual Input Properties Input: ion_mask :K+,Cl-,Na+ solute_mask :DA,DC,DG,DT,D?3,D?5 distance 6.0 overlap 4.0 binary_path cpptraj output_format crd
Step 6: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_crd_path' from step 5 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 5 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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,"restraintmask" : "\":DA,DC,DG,DT,D=3,D=5&!@H=\""} 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 7: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 6 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: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 6 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 6 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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,"restraintmask" : "\":DA,DC,DG,DT,D=3,D=5&!@H=\""} 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 9: ProcessMdout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 8 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 10: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 8 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 8 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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,"restraintmask" : "\":DA,DC,DG,DT,D=3,D=5&!@H=\""} 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 11: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 10 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 12: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_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_rst_path' from step 10 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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,"restraintmask" : "\":DA,DC,DG,DT,D=3,D=5&!@H=\""} 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 13: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 12 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 14: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 12 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 12 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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} 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 15: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 input CRD,MDCRD,INPCRD,NETCDF,NC,NCRST file Output dataset 'output_rst_path' from step 14 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 14 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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,"restraintmask" : "\":DA,DC,DG,DT,D=3,D=5&!@H=\""} 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 16: ProcessMinout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 14 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 17: 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 PRES binary_path process_mdout.perl output_format dat
Step 18: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 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.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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,"restraintmask" : "\":DA,DC,DG,DT,D=3,D=5&!@H=\""} 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: ProcessMdout input LOG,OUT,TXT,O file Output dataset 'output_log_path' from step 18 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 20: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 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.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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,"restraintmask" : "\":DA,DC,DG,DT,D=3,D=5&@P,O5'"'"',C5'"'"',C4'"'"',C3'"'"',O3'"'"'\""} 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 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 PRES DENSITY binary_path process_mdout.perl output_format dat
Step 22: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 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.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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} 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 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 PRES DENSITY binary_path process_mdout.perl output_format dat
Step 24: SanderMdrun input TOP,PARMTOP,PRMTOP file Output dataset 'output_top_path' from step 4 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.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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, "ntpr": 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 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 4 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 Output dataset 'output_rst_path' from step 24 output LOG,OUT,TXT,O name mysander_mdrun.log output TRJ,CRD,MDCRD,X,NETCDF,NC name mysander_mdrun.nc output RST,RST7,NETCDF,NC,NCRST name mysander_mdrun.ncrst 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, "ntpr": 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

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gbayarri

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ABCix MD Setup

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