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.

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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

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Frozen Version-1 c3a41d9
help Creators and Submitter
Citation
Hospital, A., & Bayarri, G. (2023). CWL ABC MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.262.2
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Created: 11th Jan 2022 at 08:14

Last updated: 17th Mar 2022 at 10:44

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