CWL ABC MD Setup tutorial

View on GitHub Download RO-Crate
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.

Click and drag the diagram to pan, double click or use the controls to zoom.

SEEK ID: https://workflowhub.eu/workflows/262?version=2

DOI: 10.48546/workflowhub.workflow.262.2

Inputs

ID Name Description Type
step1_leap_gen_top_input_pdb_path Input file Input 3D structure PDB file.
  • File
step1_leap_gen_top_output_pdb_path Output file Output 3D structure PDB file matching the topology file.
  • string
step1_leap_gen_top_output_top_path Output file Output topology file (AMBER ParmTop).
  • string
step1_leap_gen_top_output_crd_path Output file Output coordinates file (AMBER crd).
  • string
step1_leap_gen_top_config Config file Configuration file for biobb_amber.leap_gen_top tool.
  • string
step2_leap_solvate_output_pdb_path Output file Output 3D structure PDB file matching the topology file.
  • string
step2_leap_solvate_output_top_path Output file Output topology file (AMBER ParmTop).
  • string
step2_leap_solvate_output_crd_path Output file Output coordinates file (AMBER crd).
  • string
step2_leap_solvate_config Config file Configuration file for biobb_amber.leap_solvate tool.
  • string
step3_leap_add_ions_output_pdb_path Output file Output 3D structure PDB file matching the topology file.
  • string
step3_leap_add_ions_output_top_path Output file Output topology file (AMBER ParmTop).
  • string
step3_leap_add_ions_output_crd_path Output file Output coordinates file (AMBER crd).
  • string
step3_leap_add_ions_config Config file Configuration file for biobb_amber.leap_add_ions tool.
  • string
step4_cpptraj_randomize_ions_output_pdb_path Output file Structure PDB file with randomized ions.
  • string
step4_cpptraj_randomize_ions_output_crd_path Output file Structure CRD file with coordinates including randomized ions.
  • string
step4_cpptraj_randomize_ions_config Config file Configuration file for biobb_amber.cpptraj_randomize_ions tool.
  • string
step5_parmed_hmassrepartition_output_top_path Output file Output topology file (AMBER ParmTop).
  • string
step6_sander_mdrun_eq1_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step6_sander_mdrun_eq1_output_traj_path Output file Output trajectory file.
  • string
step6_sander_mdrun_eq1_output_rst_path Output file Output restart file.
  • string
step6_sander_mdrun_eq1_output_log_path Output file Output log file.
  • string
step6_sander_mdrun_eq1_output_mdinfo_path Output file Output MD info.
  • string
step6_sander_mdrun_eq1_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step7_process_minout_eq1_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step7_process_minout_eq1_config Config file Configuration file for biobb_amber.process_minout tool.
  • string
step8_sander_mdrun_eq2_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step8_sander_mdrun_eq2_output_traj_path Output file Output trajectory file.
  • string
step8_sander_mdrun_eq2_output_rst_path Output file Output restart file.
  • string
step8_sander_mdrun_eq2_output_log_path Output file Output log file.
  • string
step8_sander_mdrun_eq2_output_mdinfo_path Output file Output MD info.
  • string
step8_sander_mdrun_eq2_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step9_process_mdout_eq2_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step9_process_mdout_eq2_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step10_sander_mdrun_eq3_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step10_sander_mdrun_eq3_output_traj_path Output file Output trajectory file.
  • string
step10_sander_mdrun_eq3_output_rst_path Output file Output restart file.
  • string
step10_sander_mdrun_eq3_output_log_path Output file Output log file.
  • string
step10_sander_mdrun_eq3_output_mdinfo_path Output file Output MD info.
  • string
step10_sander_mdrun_eq3_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step11_process_minout_eq3_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step11_process_minout_eq3_config Config file Configuration file for biobb_amber.process_minout tool.
  • string
step12_sander_mdrun_eq4_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step12_sander_mdrun_eq4_output_traj_path Output file Output trajectory file.
  • string
step12_sander_mdrun_eq4_output_rst_path Output file Output restart file.
  • string
step12_sander_mdrun_eq4_output_log_path Output file Output log file.
  • string
step12_sander_mdrun_eq4_output_mdinfo_path Output file Output MD info.
  • string
step12_sander_mdrun_eq4_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step13_process_minout_eq4_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step13_process_minout_eq4_config Config file Configuration file for biobb_amber.process_minout tool.
  • string
step14_sander_mdrun_eq5_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step14_sander_mdrun_eq5_output_traj_path Output file Output trajectory file.
  • string
step14_sander_mdrun_eq5_output_rst_path Output file Output restart file.
  • string
step14_sander_mdrun_eq5_output_log_path Output file Output log file.
  • string
step14_sander_mdrun_eq5_output_mdinfo_path Output file Output MD info.
  • string
step14_sander_mdrun_eq5_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step15_process_minout_eq5_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step15_process_minout_eq5_config Config file Configuration file for biobb_amber.process_minout tool.
  • string
step16_sander_mdrun_eq6_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step16_sander_mdrun_eq6_output_traj_path Output file Output trajectory file.
  • string
step16_sander_mdrun_eq6_output_rst_path Output file Output restart file.
  • string
step16_sander_mdrun_eq6_output_log_path Output file Output log file.
  • string
step16_sander_mdrun_eq6_output_mdinfo_path Output file Output MD info.
  • string
step16_sander_mdrun_eq6_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step17_process_mdout_eq6_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step17_process_mdout_eq6_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step18_sander_mdrun_eq7_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step18_sander_mdrun_eq7_output_traj_path Output file Output trajectory file.
  • string
step18_sander_mdrun_eq7_output_rst_path Output file Output restart file.
  • string
step18_sander_mdrun_eq7_output_log_path Output file Output log file.
  • string
step18_sander_mdrun_eq7_output_mdinfo_path Output file Output MD info.
  • string
step18_sander_mdrun_eq7_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step19_process_mdout_eq7_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step19_process_mdout_eq7_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step20_sander_mdrun_eq8_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step20_sander_mdrun_eq8_output_traj_path Output file Output trajectory file.
  • string
step20_sander_mdrun_eq8_output_rst_path Output file Output restart file.
  • string
step20_sander_mdrun_eq8_output_log_path Output file Output log file.
  • string
step20_sander_mdrun_eq8_output_mdinfo_path Output file Output MD info.
  • string
step20_sander_mdrun_eq8_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step21_process_mdout_eq8_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step21_process_mdout_eq8_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step22_sander_mdrun_eq9_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step22_sander_mdrun_eq9_output_traj_path Output file Output trajectory file.
  • string
step22_sander_mdrun_eq9_output_rst_path Output file Output restart file.
  • string
step22_sander_mdrun_eq9_output_log_path Output file Output log file.
  • string
step22_sander_mdrun_eq9_output_mdinfo_path Output file Output MD info.
  • string
step22_sander_mdrun_eq9_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step23_process_mdout_eq9_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step23_process_mdout_eq9_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step24_sander_mdrun_eq10_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step24_sander_mdrun_eq10_output_traj_path Output file Output trajectory file.
  • string
step24_sander_mdrun_eq10_output_rst_path Output file Output restart file.
  • string
step24_sander_mdrun_eq10_output_log_path Output file Output log file.
  • string
step24_sander_mdrun_eq10_output_mdinfo_path Output file Output MD info.
  • string
step24_sander_mdrun_eq10_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step25_process_mdout_eq10_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step25_process_mdout_eq10_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step26_sander_mdrun_md_input_mdin_path Input file Input configuration file (MD run options) (AMBER mdin).
  • File
step26_sander_mdrun_md_output_traj_path Output file Output trajectory file.
  • string
step26_sander_mdrun_md_output_rst_path Output file Output restart file.
  • string
step26_sander_mdrun_md_output_mdinfo_path Output file Output MD info.
  • string
step26_sander_mdrun_md_output_log_path Output file Output log file.
  • string
step26_sander_mdrun_md_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step27_rmsd_first_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step27_rmsd_first_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step28_rmsd_exp_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step28_rmsd_exp_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step29_cpptraj_rgyr_output_cpptraj_path Output file Path to the output analysis.
  • string
step29_cpptraj_rgyr_config Config file Configuration file for biobb_analysis.cpptraj_rgyr tool.
  • string
step30_cpptraj_image_output_cpptraj_path Output file Path to the output processed trajectory.
  • string
step30_cpptraj_image_config Config file Configuration file for biobb_analysis.cpptraj_image tool.
  • string

Steps

ID Name Description
step1_leap_gen_top leap_gen_top Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package
step2_leap_solvate leap_solvate Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package
step3_leap_add_ions leap_add_ions Adds counterions to a system box for an AMBER MD system using tLeap tool from the AmberTools MD package
step4_cpptraj_randomize_ions cpptraj_randomize_ions Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package
step5_parmed_hmassrepartition parmed_hmassrepartition Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package
step6_sander_mdrun_eq1 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step7_process_minout_eq1 process_minout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step9_process_mdout_eq2 process_mdout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step11_process_minout_eq3 process_minout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step13_process_minout_eq4 process_minout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step15_process_minout_eq5 process_minout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step17_process_mdout_eq6 process_mdout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step19_process_mdout_eq7 process_mdout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step21_process_mdout_eq8 process_mdout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step23_process_mdout_eq9 process_mdout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step25_process_mdout_eq10 process_mdout 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 sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step27_rmsd_first cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step28_rmsd_exp cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step29_cpptraj_rgyr cpptraj_rgyr Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
step30_cpptraj_image cpptraj_image Wrapper of the Ambertools Cpptraj module for correcting periodicity (image) from a given cpptraj trajectory file.

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
step27_rmsd_first_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step28_rmsd_exp_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step29_cpptraj_rgyr_out1 output_cpptraj_path Path to the output analysis.
  • File
step30_cpptraj_image_out1 output_cpptraj_path Path to the output processed trajectory.
  • File

Version History

Version 2 (latest) Created 12th Jun 2023 at 09:27 by Genís Bayarri

Updated workflow descriptors


Frozen Version-2 62d05f1

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

No revision comments

Frozen Version-1 c3a41d9
help Creators and Submitter
Creators
Submitter
Discussion Channels
BioExcel Workflows
Tutorial
Documentation
Citation
Hospital, A., & Bayarri, G. (2023). CWL ABC MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.262.2
License
Apache License 2.0
Activity

Views: 2778   Downloads: 627

Created: 11th Jan 2022 at 08:14

Last updated: 17th Mar 2022 at 10:44

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 169 KB
Powered by
 (v.1.16.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH