CWL Amber Protein Ligand Complex 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.

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SEEK ID: https://workflowhub.eu/workflows/261?version=2

DOI: 10.48546/workflowhub.workflow.261.2

Inputs

ID Name Description Type
step000_reduce_remove_hydrogens_input_path Input file Path to the input file.
  • File
step000_reduce_remove_hydrogens_output_path Output file Path to the output file.
  • string
step00_extract_molecule_output_molecule_path Output file Output molecule file path.
  • string
step0000_cat_pdb_input_structure2 Input file Input structure 2 file path.
  • File
step0000_cat_pdb_output_structure_path Output file Output protein file path.
  • string
step0_cat_pdb_input_structure2 Input file Input structure 2 file path.
  • File
step0_cat_pdb_output_structure_path Output file Output protein file path.
  • string
step1_pdb4amber_run_output_pdb_path Output file Output 3D structure PDB file.
  • string
step2_leap_gen_top_input_lib_path Input file Input ligand library parameters file.
  • File
step2_leap_gen_top_input_frcmod_path Input file Input ligand frcmod parameters file.
  • File
step2_leap_gen_top_output_pdb_path Output file Output 3D structure PDB file matching the topology file.
  • string
step2_leap_gen_top_output_top_path Output file Output topology file (AMBER ParmTop).
  • string
step2_leap_gen_top_output_crd_path Output file Output coordinates file (AMBER crd).
  • string
step2_leap_gen_top_config Config file Configuration file for biobb_amber.leap_gen_top tool.
  • string
step3_sander_mdrun_minH_output_traj_path Output file Output trajectory file.
  • string
step3_sander_mdrun_minH_output_rst_path Output file Output restart file.
  • string
step3_sander_mdrun_minH_output_log_path Output file Output log file.
  • string
step3_sander_mdrun_minH_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step4_process_minout_minH_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step4_process_minout_minH_config Config file Configuration file for biobb_amber.process_minout tool.
  • string
step5_sander_mdrun_min_output_traj_path Output file Output trajectory file.
  • string
step5_sander_mdrun_min_output_rst_path Output file Output restart file.
  • string
step5_sander_mdrun_min_output_log_path Output file Output log file.
  • string
step5_sander_mdrun_min_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step6_process_minout_min_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step6_process_minout_min_config Config file Configuration file for biobb_amber.process_minout tool.
  • string
step7_amber_to_pdb_output_pdb_path Output file Structure PDB file.
  • string
step8_leap_solvate_input_lib_path Input file Input ligand library parameters file.
  • File
step8_leap_solvate_input_frcmod_path Input file Input ligand frcmod parameters file.
  • File
step8_leap_solvate_output_pdb_path Output file Output 3D structure PDB file matching the topology file.
  • string
step8_leap_solvate_output_top_path Output file Output topology file (AMBER ParmTop).
  • string
step8_leap_solvate_output_crd_path Output file Output coordinates file (AMBER crd).
  • string
step8_leap_solvate_config Config file Configuration file for biobb_amber.leap_solvate tool.
  • string
step9_leap_add_ions_input_lib_path Input file Input ligand library parameters file.
  • File
step9_leap_add_ions_input_frcmod_path Input file Input ligand frcmod parameters file.
  • File
step9_leap_add_ions_output_pdb_path Output file Output 3D structure PDB file matching the topology file.
  • string
step9_leap_add_ions_output_top_path Output file Output topology file (AMBER ParmTop).
  • string
step9_leap_add_ions_output_crd_path Output file Output coordinates file (AMBER crd).
  • string
step9_leap_add_ions_config Config file Configuration file for biobb_amber.leap_add_ions tool.
  • string
step10_sander_mdrun_energy_output_traj_path Output file Output trajectory file.
  • string
step10_sander_mdrun_energy_output_rst_path Output file Output restart file.
  • string
step10_sander_mdrun_energy_output_log_path Output file Output log file.
  • string
step10_sander_mdrun_energy_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step11_process_minout_energy_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step11_process_minout_energy_config Config file Configuration file for biobb_amber.process_minout tool.
  • string
step12_sander_mdrun_warm_output_traj_path Output file Output trajectory file.
  • string
step12_sander_mdrun_warm_output_rst_path Output file Output restart file.
  • string
step12_sander_mdrun_warm_output_log_path Output file Output log file.
  • string
step12_sander_mdrun_warm_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step13_process_mdout_warm_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step13_process_mdout_warm_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step14_sander_mdrun_nvt_output_traj_path Output file Output trajectory file.
  • string
step14_sander_mdrun_nvt_output_rst_path Output file Output restart file.
  • string
step14_sander_mdrun_nvt_output_log_path Output file Output log file.
  • string
step14_sander_mdrun_nvt_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step15_process_mdout_nvt_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step15_process_mdout_nvt_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step16_sander_mdrun_npt_output_traj_path Output file Output trajectory file.
  • string
step16_sander_mdrun_npt_output_rst_path Output file Output restart file.
  • string
step16_sander_mdrun_npt_output_log_path Output file Output log file.
  • string
step16_sander_mdrun_npt_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step17_process_mdout_npt_output_dat_path Output file Dat output file containing data from the specified terms along the minimization process.
  • string
step17_process_mdout_npt_config Config file Configuration file for biobb_amber.process_mdout tool.
  • string
step18_sander_mdrun_md_output_traj_path Output file Output trajectory file.
  • string
step18_sander_mdrun_md_output_rst_path Output file Output restart file.
  • string
step18_sander_mdrun_md_output_log_path Output file Output log file.
  • string
step18_sander_mdrun_md_config Config file Configuration file for biobb_amber.sander_mdrun tool.
  • string
step19_rmsd_first_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step19_rmsd_first_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step20_rmsd_exp_output_cpptraj_path Output file Path to the output processed analysis.
  • string
step20_rmsd_exp_config Config file Configuration file for biobb_analysis.cpptraj_rms tool.
  • string
step21_cpptraj_rgyr_output_cpptraj_path Output file Path to the output analysis.
  • string
step21_cpptraj_rgyr_config Config file Configuration file for biobb_analysis.cpptraj_rgyr tool.
  • string
step22_cpptraj_image_output_cpptraj_path Output file Path to the output processed trajectory.
  • string
step22_cpptraj_image_config Config file Configuration file for biobb_analysis.cpptraj_image tool.
  • string

Steps

ID Name Description
step000_reduce_remove_hydrogens reduce_remove_hydrogens Removes hydrogen atoms to small molecules.
step00_extract_molecule extract_molecule This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.
step0000_cat_pdb cat_pdb Class to concat two PDB structures in a single PDB file.
step0_cat_pdb cat_pdb Class to concat two PDB structures in a single PDB file.
step1_pdb4amber_run pdb4amber_run Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package
step2_leap_gen_top leap_gen_top Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package
step3_sander_mdrun_minH sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step4_process_minout_minH 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
step5_sander_mdrun_min sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step6_process_minout_min 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
step7_amber_to_pdb amber_to_pdb Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package
step8_leap_solvate leap_solvate Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package
step9_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
step10_sander_mdrun_energy sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step11_process_minout_energy 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_warm sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step13_process_mdout_warm 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
step14_sander_mdrun_nvt sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step15_process_mdout_nvt 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
step16_sander_mdrun_npt sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step17_process_mdout_npt 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_md sander_mdrun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step19_rmsd_first cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step20_rmsd_exp cpptraj_rms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step21_cpptraj_rgyr cpptraj_rgyr Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
step22_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
step000_reduce_remove_hydrogens_out1 output_path Path to the output file.
  • File
step00_extract_molecule_out1 output_molecule_path Output molecule file path.
  • File
step0000_cat_pdb_out1 output_structure_path Output protein file path.
  • File
step0_cat_pdb_out1 output_structure_path Output protein file path.
  • File
step1_pdb4amber_run_out1 output_pdb_path Output 3D structure PDB file.
  • File
step2_leap_gen_top_out1 output_pdb_path Output 3D structure PDB file matching the topology file.
  • File
step2_leap_gen_top_out2 output_top_path Output topology file (AMBER ParmTop).
  • File
step2_leap_gen_top_out3 output_crd_path Output coordinates file (AMBER crd).
  • File
step3_sander_mdrun_minH_out1 output_traj_path Output trajectory file.
  • File
step3_sander_mdrun_minH_out2 output_rst_path Output restart file.
  • File
step3_sander_mdrun_minH_out3 output_log_path Output log file.
  • File
step4_process_minout_minH_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process.
  • File
step5_sander_mdrun_min_out1 output_traj_path Output trajectory file.
  • File
step5_sander_mdrun_min_out2 output_rst_path Output restart file.
  • File
step5_sander_mdrun_min_out3 output_log_path Output log file.
  • File
step6_process_minout_min_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process.
  • File
step7_amber_to_pdb_out1 output_pdb_path Structure PDB file.
  • File
step8_leap_solvate_out1 output_pdb_path Output 3D structure PDB file matching the topology file.
  • File
step8_leap_solvate_out2 output_top_path Output topology file (AMBER ParmTop).
  • File
step8_leap_solvate_out3 output_crd_path Output coordinates file (AMBER crd).
  • File
step9_leap_add_ions_out1 output_pdb_path Output 3D structure PDB file matching the topology file.
  • File
step9_leap_add_ions_out2 output_top_path Output topology file (AMBER ParmTop).
  • File
step9_leap_add_ions_out3 output_crd_path Output coordinates file (AMBER crd).
  • File
step10_sander_mdrun_energy_out1 output_traj_path Output trajectory file.
  • File
step10_sander_mdrun_energy_out2 output_rst_path Output restart file.
  • File
step10_sander_mdrun_energy_out3 output_log_path Output log file.
  • File
step11_process_minout_energy_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process.
  • File
step12_sander_mdrun_warm_out1 output_traj_path Output trajectory file.
  • File
step12_sander_mdrun_warm_out2 output_rst_path Output restart file.
  • File
step12_sander_mdrun_warm_out3 output_log_path Output log file.
  • File
step13_process_mdout_warm_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process.
  • File
step14_sander_mdrun_nvt_out1 output_traj_path Output trajectory file.
  • File
step14_sander_mdrun_nvt_out2 output_rst_path Output restart file.
  • File
step14_sander_mdrun_nvt_out3 output_log_path Output log file.
  • File
step15_process_mdout_nvt_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process.
  • File
step16_sander_mdrun_npt_out1 output_traj_path Output trajectory file.
  • File
step16_sander_mdrun_npt_out2 output_rst_path Output restart file.
  • File
step16_sander_mdrun_npt_out3 output_log_path Output log file.
  • File
step17_process_mdout_npt_out1 output_dat_path Dat output file containing data from the specified terms along the minimization process.
  • File
step18_sander_mdrun_md_out1 output_traj_path Output trajectory file.
  • File
step18_sander_mdrun_md_out2 output_rst_path Output restart file.
  • File
step18_sander_mdrun_md_out3 output_log_path Output log file.
  • File
step19_rmsd_first_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step20_rmsd_exp_out1 output_cpptraj_path Path to the output processed analysis.
  • File
step21_cpptraj_rgyr_out1 output_cpptraj_path Path to the output analysis.
  • File
step22_cpptraj_image_out1 output_cpptraj_path Path to the output processed trajectory.
  • File

Version History

Version 2 (latest) Created 9th Jun 2023 at 07:44 by Genís Bayarri

Updated workflow descriptors


Frozen Version-2 b9eafdb

Version 1 (earliest) Created 10th Jan 2022 at 15:27 by Genís Bayarri

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Frozen Version-1 c9cd8a7
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Citation
Hospital, A., & Bayarri, G. (2023). CWL Amber Protein Ligand Complex MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.261.2
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Views: 2960   Downloads: 634

Created: 10th Jan 2022 at 15:27

Last updated: 17th Mar 2022 at 10:35

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