CWL Amber Protein 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/260?version=1

DOI: 10.48546/workflowhub.workflow.260.1

Inputs

ID Name Description Type
step0_extract_molecule_input_structure_path n/a n/a
  • File
step0_extract_molecule_output_molecule_path n/a n/a
  • string
step1_pdb4amber_run_output_pdb_path n/a n/a
  • string
step2_leap_gen_top_config n/a n/a
  • string
step2_leap_gen_top_output_pdb_path n/a n/a
  • string
step2_leap_gen_top_output_top_path n/a n/a
  • string
step2_leap_gen_top_output_crd_path n/a n/a
  • string
step3_sander_mdrun_minH_config n/a n/a
  • string
step3_sander_mdrun_minH_output_traj_path n/a n/a
  • string
step3_sander_mdrun_minH_output_rst_path n/a n/a
  • string
step3_sander_mdrun_minH_output_log_path n/a n/a
  • string
step4_process_minout_minH_config n/a n/a
  • string
step4_process_minout_minH_output_dat_path n/a n/a
  • string
step5_sander_mdrun_min_config n/a n/a
  • string
step5_sander_mdrun_min_output_traj_path n/a n/a
  • string
step5_sander_mdrun_min_output_rst_path n/a n/a
  • string
step5_sander_mdrun_min_output_log_path n/a n/a
  • string
step6_process_minout_min_config n/a n/a
  • string
step6_process_minout_min_output_dat_path n/a n/a
  • string
step7_amber_to_pdb_output_pdb_path n/a n/a
  • string
step8_leap_solvate_config n/a n/a
  • string
step8_leap_solvate_output_pdb_path n/a n/a
  • string
step8_leap_solvate_output_top_path n/a n/a
  • string
step8_leap_solvate_output_crd_path n/a n/a
  • string
step9_leap_add_ions_config n/a n/a
  • string
step9_leap_add_ions_output_pdb_path n/a n/a
  • string
step9_leap_add_ions_output_top_path n/a n/a
  • string
step9_leap_add_ions_output_crd_path n/a n/a
  • string
step10_sander_mdrun_energy_config n/a n/a
  • string
step10_sander_mdrun_energy_output_traj_path n/a n/a
  • string
step10_sander_mdrun_energy_output_rst_path n/a n/a
  • string
step10_sander_mdrun_energy_output_log_path n/a n/a
  • string
step11_process_minout_energy_config n/a n/a
  • string
step11_process_minout_energy_output_dat_path n/a n/a
  • string
step12_sander_mdrun_warm_config n/a n/a
  • string
step12_sander_mdrun_warm_output_traj_path n/a n/a
  • string
step12_sander_mdrun_warm_output_rst_path n/a n/a
  • string
step12_sander_mdrun_warm_output_log_path n/a n/a
  • string
step13_process_mdout_warm_config n/a n/a
  • string
step13_process_mdout_warm_output_dat_path n/a n/a
  • string
step14_sander_mdrun_nvt_config n/a n/a
  • string
step14_sander_mdrun_nvt_output_traj_path n/a n/a
  • string
step14_sander_mdrun_nvt_output_rst_path n/a n/a
  • string
step14_sander_mdrun_nvt_output_log_path n/a n/a
  • string
step15_process_mdout_nvt_config n/a n/a
  • string
step15_process_mdout_nvt_output_dat_path n/a n/a
  • string
step16_sander_mdrun_npt_config n/a n/a
  • string
step16_sander_mdrun_npt_output_traj_path n/a n/a
  • string
step16_sander_mdrun_npt_output_rst_path n/a n/a
  • string
step16_sander_mdrun_npt_output_log_path n/a n/a
  • string
step17_process_mdout_npt_config n/a n/a
  • string
step17_process_mdout_npt_output_dat_path n/a n/a
  • string
step18_sander_mdrun_md_config n/a n/a
  • string
step18_sander_mdrun_md_output_traj_path n/a n/a
  • string
step18_sander_mdrun_md_output_rst_path n/a n/a
  • string
step18_sander_mdrun_md_output_log_path n/a n/a
  • string
step19_rmsd_first_config n/a n/a
  • string
step19_rmsd_first_output_cpptraj_path n/a n/a
  • string
step20_rmsd_exp_config n/a n/a
  • string
step20_rmsd_exp_input_exp_path n/a n/a
  • File
step20_rmsd_exp_output_cpptraj_path n/a n/a
  • string
step21_cpptraj_rgyr_config n/a n/a
  • string
step21_cpptraj_rgyr_output_cpptraj_path n/a n/a
  • string
step22_cpptraj_image_config n/a n/a
  • string
step22_cpptraj_image_output_cpptraj_path n/a n/a
  • string

Steps

ID Name Description
step0_extract_molecule ExtractMolecule This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.
step1_pdb4amber_run Pdb4amberRun 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 LeapGenTop Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package
step3_sander_mdrun_minH SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step4_process_minout_minH 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
step5_sander_mdrun_min SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step6_process_minout_min 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
step7_amber_to_pdb AmberToPDB Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package
step8_leap_solvate LeapSolvate Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package
step9_leap_add_ions LeapAddIons Adds counterions to a system box for an AMBER MD system using tLeap tool from the AmberTools MD package
step10_sander_mdrun_energy SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step11_process_minout_energy 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_warm SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step13_process_mdout_warm 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
step14_sander_mdrun_nvt SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step15_process_mdout_nvt 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
step16_sander_mdrun_npt SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step17_process_mdout_npt 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_md SanderMDRun Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package
step19_rmsd_first CpptrajRms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step20_rmsd_exp CpptrajRms Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
step21_cpptraj_rgyr CpptrajRgyr Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
step22_cpptraj_image CpptrajImage Wrapper of the Ambertools Cpptraj module for correcting periodicity (image) from a given cpptraj trajectory file.

Outputs

ID Name Description Type
step0_extract_molecule_out1 output_molecule_path Output molecule 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 1 (earliest) Created 10th Jan 2022 at 13:24 by Genís Bayarri

Fetched structure.pdb from URL


Open master 569bbc9
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Citation
Bayarri, G., & Hospital, A. (2022). AMBER Protein MD Setup. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.260.1
License
Apache Software License 2.0
Activity

Views: 651   Downloads: 2

Created: 10th Jan 2022 at 13:24

Last updated: 17th Mar 2022 at 10:24

Last used: 27th Nov 2022 at 07:32

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