CWL Amber Protein Ligand Complex MD Setup tutorial
Version 1

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.

Inputs

ID Name Description Type
step00_extract_molecule_input_structure_path n/a n/a
  • File
step00_extract_molecule_output_molecule_path n/a n/a
  • string
step0_cat_pdb_input_structure2 n/a n/a
  • File
step0_cat_pdb_output_structure_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_input_lib_path n/a n/a
  • File
step2_leap_gen_top_input_frcmod_path n/a n/a
  • File
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_input_lib_path n/a n/a
  • File
step8_leap_solvate_input_frcmod_path n/a n/a
  • File
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_input_lib_path n/a n/a
  • File
step9_leap_add_ions_input_frcmod_path n/a n/a
  • File
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_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
step00_extract_molecule ExtractMolecule This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.
step0_cat_pdb CatPDB Class to concat two PDB structures in a single PDB file.
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
step00_extract_molecule_out1 output_molecule_path Output molecule 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 1 (earliest) Created 10th Jan 2022 at 15:27 by Genís Bayarri

Fetched structure.pdb from URL


Open master c9cd8a7
help Creators and Submitter
Citation
Bayarri, G., & Hospital, A. (2022). AMBER Protein Ligand Complex MD Setup. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.261.1
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Views: 463   Downloads: 4

Created: 10th Jan 2022 at 15:27

Last updated: 17th Mar 2022 at 10:35

Last used: 28th Jun 2022 at 16:02

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