CWL ABC MD Setup tutorial
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AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

Licensed under the Apache License 2.0, see the file LICENSE for details.

SEEK ID: https://workflowhub.eu/workflows/262?version=1

DOI: 10.48546/workflowhub.workflow.262.1

Inputs

ID Name Description Type
step1_leap_gen_top_config n/a n/a
  • string
step1_leap_gen_top_input_pdb_path n/a n/a
  • File
step1_leap_gen_top_output_pdb_path n/a n/a
  • string
step1_leap_gen_top_output_top_path n/a n/a
  • string
step1_leap_gen_top_output_crd_path n/a n/a
  • string
step2_leap_solvate_config n/a n/a
  • string
step2_leap_solvate_output_pdb_path n/a n/a
  • string
step2_leap_solvate_output_top_path n/a n/a
  • string
step2_leap_solvate_output_crd_path n/a n/a
  • string
step3_leap_add_ions_config n/a n/a
  • string
step3_leap_add_ions_output_pdb_path n/a n/a
  • string
step3_leap_add_ions_output_top_path n/a n/a
  • string
step3_leap_add_ions_output_crd_path n/a n/a
  • string
step4_cpptraj_randomize_ions_config n/a n/a
  • string
step4_cpptraj_randomize_ions_output_pdb_path n/a n/a
  • string
step4_cpptraj_randomize_ions_output_crd_path n/a n/a
  • string
step5_parmed_hmassrepartition_output_top_path n/a n/a
  • string
step6_sander_mdrun_eq1_config n/a n/a
  • string
step6_sander_mdrun_eq1_input_mdin_path n/a n/a
  • File
step6_sander_mdrun_eq1_output_traj_path n/a n/a
  • string
step6_sander_mdrun_eq1_output_rst_path n/a n/a
  • string
step6_sander_mdrun_eq1_output_log_path n/a n/a
  • string
step6_sander_mdrun_eq1_output_mdinfo_path n/a n/a
  • string
step7_process_minout_eq1_config n/a n/a
  • string
step7_process_minout_eq1_output_dat_path n/a n/a
  • string
step8_sander_mdrun_eq2_config n/a n/a
  • string
step8_sander_mdrun_eq2_input_mdin_path n/a n/a
  • File
step8_sander_mdrun_eq2_output_traj_path n/a n/a
  • string
step8_sander_mdrun_eq2_output_rst_path n/a n/a
  • string
step8_sander_mdrun_eq2_output_log_path n/a n/a
  • string
step8_sander_mdrun_eq2_output_mdinfo_path n/a n/a
  • string
step9_process_mdout_eq2_config n/a n/a
  • string
step9_process_mdout_eq2_output_dat_path n/a n/a
  • string
step10_sander_mdrun_eq3_config n/a n/a
  • string
step10_sander_mdrun_eq3_input_mdin_path n/a n/a
  • File
step10_sander_mdrun_eq3_output_traj_path n/a n/a
  • string
step10_sander_mdrun_eq3_output_rst_path n/a n/a
  • string
step10_sander_mdrun_eq3_output_log_path n/a n/a
  • string
step10_sander_mdrun_eq3_output_mdinfo_path n/a n/a
  • string
step11_process_minout_eq3_config n/a n/a
  • string
step11_process_minout_eq3_output_dat_path n/a n/a
  • string
step12_sander_mdrun_eq4_config n/a n/a
  • string
step12_sander_mdrun_eq4_input_mdin_path n/a n/a
  • File
step12_sander_mdrun_eq4_output_traj_path n/a n/a
  • string
step12_sander_mdrun_eq4_output_rst_path n/a n/a
  • string
step12_sander_mdrun_eq4_output_log_path n/a n/a
  • string
step12_sander_mdrun_eq4_output_mdinfo_path n/a n/a
  • string
step13_process_minout_eq4_config n/a n/a
  • string
step13_process_minout_eq4_output_dat_path n/a n/a
  • string
step14_sander_mdrun_eq5_config n/a n/a
  • string
step14_sander_mdrun_eq5_input_mdin_path n/a n/a
  • File
step14_sander_mdrun_eq5_output_traj_path n/a n/a
  • string
step14_sander_mdrun_eq5_output_rst_path n/a n/a
  • string
step14_sander_mdrun_eq5_output_log_path n/a n/a
  • string
step14_sander_mdrun_eq5_output_mdinfo_path n/a n/a
  • string
step15_process_minout_eq5_config n/a n/a
  • string
step15_process_minout_eq5_output_dat_path n/a n/a
  • string
step16_sander_mdrun_eq6_config n/a n/a
  • string
step16_sander_mdrun_eq6_input_mdin_path n/a n/a
  • File
step16_sander_mdrun_eq6_output_traj_path n/a n/a
  • string
step16_sander_mdrun_eq6_output_rst_path n/a n/a
  • string
step16_sander_mdrun_eq6_output_log_path n/a n/a
  • string
step16_sander_mdrun_eq6_output_mdinfo_path n/a n/a
  • string
step17_process_mdout_eq6_config n/a n/a
  • string
step17_process_mdout_eq6_output_dat_path n/a n/a
  • string
step18_sander_mdrun_eq7_config n/a n/a
  • string
step18_sander_mdrun_eq7_input_mdin_path n/a n/a
  • File
step18_sander_mdrun_eq7_output_traj_path n/a n/a
  • string
step18_sander_mdrun_eq7_output_rst_path n/a n/a
  • string
step18_sander_mdrun_eq7_output_log_path n/a n/a
  • string
step18_sander_mdrun_eq7_output_mdinfo_path n/a n/a
  • string
step19_process_mdout_eq7_config n/a n/a
  • string
step19_process_mdout_eq7_output_dat_path n/a n/a
  • string
step20_sander_mdrun_eq8_config n/a n/a
  • string
step20_sander_mdrun_eq8_input_mdin_path n/a n/a
  • File
step20_sander_mdrun_eq8_output_traj_path n/a n/a
  • string
step20_sander_mdrun_eq8_output_rst_path n/a n/a
  • string
step20_sander_mdrun_eq8_output_log_path n/a n/a
  • string
step20_sander_mdrun_eq8_output_mdinfo_path n/a n/a
  • string
step21_process_mdout_eq8_config n/a n/a
  • string
step21_process_mdout_eq8_output_dat_path n/a n/a
  • string
step22_sander_mdrun_eq9_config n/a n/a
  • string
step22_sander_mdrun_eq9_input_mdin_path n/a n/a
  • File
step22_sander_mdrun_eq9_output_traj_path n/a n/a
  • string
step22_sander_mdrun_eq9_output_rst_path n/a n/a
  • string
step22_sander_mdrun_eq9_output_log_path n/a n/a
  • string
step22_sander_mdrun_eq9_output_mdinfo_path n/a n/a
  • string
step23_process_mdout_eq9_config n/a n/a
  • string
step23_process_mdout_eq9_output_dat_path n/a n/a
  • string
step24_sander_mdrun_eq10_config n/a n/a
  • string
step24_sander_mdrun_eq10_input_mdin_path n/a n/a
  • File
step24_sander_mdrun_eq10_output_traj_path n/a n/a
  • string
step24_sander_mdrun_eq10_output_rst_path n/a n/a
  • string
step24_sander_mdrun_eq10_output_log_path n/a n/a
  • string
step24_sander_mdrun_eq10_output_mdinfo_path n/a n/a
  • string
step25_process_mdout_eq10_config n/a n/a
  • string
step25_process_mdout_eq10_output_dat_path n/a n/a
  • string
step26_sander_mdrun_md_config n/a n/a
  • string
step26_sander_mdrun_md_input_mdin_path n/a n/a
  • File
step26_sander_mdrun_md_output_traj_path n/a n/a
  • string
step26_sander_mdrun_md_output_rst_path n/a n/a
  • string
step26_sander_mdrun_md_output_mdinfo_path n/a n/a
  • string
step26_sander_mdrun_md_output_log_path n/a n/a
  • string

Steps

ID Name Description
step1_leap_gen_top LeapGenTop Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package
step2_leap_solvate LeapSolvate Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package
step3_leap_add_ions LeapAddIons Adds counterions to a system box for an AMBER MD system using tLeap tool from the AmberTools MD package
step4_cpptraj_randomize_ions CpptrajRandomizeIons Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package
step5_parmed_hmassrepartition ParmedHMassRepartition Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package
step6_sander_mdrun_eq1 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step7_process_minout_eq1 ProcessMinOut Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package
step8_sander_mdrun_eq2 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step9_process_mdout_eq2 ProcessMDOut Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package
step10_sander_mdrun_eq3 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step11_process_minout_eq3 ProcessMinOut Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package
step12_sander_mdrun_eq4 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step13_process_minout_eq4 ProcessMinOut Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package
step14_sander_mdrun_eq5 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step15_process_minout_eq5 ProcessMinOut Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package
step16_sander_mdrun_eq6 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step17_process_mdout_eq6 ProcessMDOut Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package
step18_sander_mdrun_eq7 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step19_process_mdout_eq7 ProcessMDOut Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package
step20_sander_mdrun_eq8 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step21_process_mdout_eq8 ProcessMDOut Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package
step22_sander_mdrun_eq9 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step23_process_mdout_eq9 ProcessMDOut Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package
step24_sander_mdrun_eq10 SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step25_process_mdout_eq10 ProcessMDOut Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package
step26_sander_mdrun_md SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package

Outputs

ID Name Description Type
step1_leap_gen_top_out1 output_pdb_path Output 3D structure PDB file matching the topology file
  • File
step1_leap_gen_top_out2 output_top_path Output topology file (AMBER ParmTop)
  • File
step1_leap_gen_top_out3 output_crd_path Output coordinates file (AMBER crd)
  • File
step2_leap_solvate_out1 output_pdb_path Output 3D structure PDB file matching the topology file
  • File
step2_leap_solvate_out2 output_top_path Output topology file (AMBER ParmTop)
  • File
step2_leap_solvate_out3 output_crd_path Output coordinates file (AMBER crd)
  • File
step3_leap_add_ions_out1 output_pdb_path Output 3D structure PDB file matching the topology file
  • File
step3_leap_add_ions_out2 output_top_path Output topology file (AMBER ParmTop)
  • File
step3_leap_add_ions_out3 output_crd_path Output coordinates file (AMBER crd)
  • File
step4_cpptraj_randomize_ions_out1 output_pdb_path Structure PDB file with randomized ions
  • File
step4_cpptraj_randomize_ions_out2 output_crd_path Structure CRD file with coordinates including randomized ions
  • File
step5_parmed_hmassrepartition_out1 output_top_path Output topology file (AMBER ParmTop)
  • File
step6_sander_mdrun_eq1_out1 output_traj_path Output trajectory file
  • File
step6_sander_mdrun_eq1_out2 output_rst_path Output restart file
  • File
step6_sander_mdrun_eq1_out3 output_log_path Output log file
  • File
step6_sander_mdrun_eq1_out4 output_mdinfo_path Output MD info
  • File
step7_process_minout_eq1_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step8_sander_mdrun_eq2_out1 output_traj_path Output trajectory file
  • File
step8_sander_mdrun_eq2_out2 output_rst_path Output restart file
  • File
step8_sander_mdrun_eq2_out3 output_log_path Output log file
  • File
step8_sander_mdrun_eq2_out4 output_mdinfo_path Output MD info
  • File
step9_process_mdout_eq2_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step10_sander_mdrun_eq3_out1 output_traj_path Output trajectory file
  • File
step10_sander_mdrun_eq3_out2 output_rst_path Output restart file
  • File
step10_sander_mdrun_eq3_out3 output_log_path Output log file
  • File
step10_sander_mdrun_eq3_out4 output_mdinfo_path Output MD info
  • File
step11_process_minout_eq3_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step12_sander_mdrun_eq4_out1 output_traj_path Output trajectory file
  • File
step12_sander_mdrun_eq4_out2 output_rst_path Output restart file
  • File
step12_sander_mdrun_eq4_out3 output_log_path Output log file
  • File
step12_sander_mdrun_eq4_out4 output_mdinfo_path Output MD info
  • File
step13_process_minout_eq4_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step14_sander_mdrun_eq5_out1 output_traj_path Output trajectory file
  • File
step14_sander_mdrun_eq5_out2 output_rst_path Output restart file
  • File
step14_sander_mdrun_eq5_out3 output_log_path Output log file
  • File
step14_sander_mdrun_eq5_out4 output_mdinfo_path Output MD info
  • File
step15_process_minout_eq5_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step16_sander_mdrun_eq6_out1 output_traj_path Output trajectory file
  • File
step16_sander_mdrun_eq6_out2 output_rst_path Output restart file
  • File
step16_sander_mdrun_eq6_out3 output_log_path Output log file
  • File
step16_sander_mdrun_eq6_out4 output_mdinfo_path Output MD info
  • File
step17_process_mdout_eq6_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step18_sander_mdrun_eq7_out1 output_traj_path Output trajectory file
  • File
step18_sander_mdrun_eq7_out2 output_rst_path Output restart file
  • File
step18_sander_mdrun_eq7_out3 output_log_path Output log file
  • File
step18_sander_mdrun_eq7_out4 output_mdinfo_path Output MD info
  • File
step19_process_mdout_eq7_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step20_sander_mdrun_eq8_out1 output_traj_path Output trajectory file
  • File
step20_sander_mdrun_eq8_out2 output_rst_path Output restart file
  • File
step20_sander_mdrun_eq8_out3 output_log_path Output log file
  • File
step20_sander_mdrun_eq8_out4 output_mdinfo_path Output MD info
  • File
step21_process_mdout_eq8_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step22_sander_mdrun_eq9_out1 output_traj_path Output trajectory file
  • File
step22_sander_mdrun_eq9_out2 output_rst_path Output restart file
  • File
step22_sander_mdrun_eq9_out3 output_log_path Output log file
  • File
step22_sander_mdrun_eq9_out4 output_mdinfo_path Output MD info
  • File
step23_process_mdout_eq9_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step24_sander_mdrun_eq10_out1 output_traj_path Output trajectory file
  • File
step24_sander_mdrun_eq10_out2 output_rst_path Output restart file
  • File
step24_sander_mdrun_eq10_out3 output_log_path Output log file
  • File
step24_sander_mdrun_eq10_out4 output_mdinfo_path Output MD info
  • File
step25_process_mdout_eq10_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process
  • File
step26_sander_mdrun_md_out1 output_traj_path Output trajectory file
  • File
step26_sander_mdrun_md_out2 output_rst_path Output restart file
  • File
step26_sander_mdrun_md_out3 output_mdinfo_path Output MD info
  • File
step26_sander_mdrun_md_out4 output_log_path Output log file
  • File

Version History

Version 1 (earliest) Created 11th Jan 2022 at 08:14 by Genís Bayarri

Fetched sequence.pdb from URL


Open master c3a41d9
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Citation
Bayarri, G., & Hospital, A. (2022). ABC MD Setup pipeline. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.262.1
License
Apache Software License 2.0
Activity

Views: 607   Downloads: 3

Created: 11th Jan 2022 at 08:14

Last updated: 17th Mar 2022 at 10:44

Last used: 11th Aug 2022 at 23:23

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