CWL ABC MD Setup tutorial
Version 1

Workflow Type: Common Workflow Language
Stable

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.

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
help Creators and Submitter
Citation
Bayarri, G., & Hospital, A. (2022). ABC MD Setup pipeline. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.262.1
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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