CWL Amber Protein Ligand Complex 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/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

No revision comments

Frozen Version-1 c9cd8a7
help Creators and Submitter
Creators
Submitter
Discussion Channels
BioExcel Workflows
Tutorial
Documentation
Citation
Hospital, A., & Bayarri, G. (2023). CWL Amber Protein Ligand Complex MD Setup tutorial. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.261.2
License
Apache Software License 2.0
Activity

Views: 1999

Created: 10th Jan 2022 at 15:27

Last updated: 17th Mar 2022 at 10:35

help Tags

This item has not yet been tagged.

help Attributions

None

Total size: 250 KB
Powered by
 (v.1.14.1)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH