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).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Inputs
ID | Name | Description | Type |
---|---|---|---|
step0_extract_molecule_input_structure_path | n/a | n/a |
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step0_extract_molecule_output_molecule_path | n/a | n/a |
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step1_pdb4amber_run_output_pdb_path | n/a | n/a |
|
step2_leap_gen_top_config | n/a | n/a |
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step2_leap_gen_top_output_pdb_path | n/a | n/a |
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step2_leap_gen_top_output_top_path | n/a | n/a |
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step2_leap_gen_top_output_crd_path | n/a | n/a |
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step3_sander_mdrun_minH_config | n/a | n/a |
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step3_sander_mdrun_minH_output_traj_path | n/a | n/a |
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step3_sander_mdrun_minH_output_rst_path | n/a | n/a |
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step3_sander_mdrun_minH_output_log_path | n/a | n/a |
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step4_process_minout_minH_config | n/a | n/a |
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step4_process_minout_minH_output_dat_path | n/a | n/a |
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step5_sander_mdrun_min_config | n/a | n/a |
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step5_sander_mdrun_min_output_traj_path | n/a | n/a |
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step5_sander_mdrun_min_output_rst_path | n/a | n/a |
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step5_sander_mdrun_min_output_log_path | n/a | n/a |
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step6_process_minout_min_config | n/a | n/a |
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step6_process_minout_min_output_dat_path | n/a | n/a |
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step7_amber_to_pdb_output_pdb_path | n/a | n/a |
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step8_leap_solvate_config | n/a | n/a |
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step8_leap_solvate_output_pdb_path | n/a | n/a |
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step8_leap_solvate_output_top_path | n/a | n/a |
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step8_leap_solvate_output_crd_path | n/a | n/a |
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step9_leap_add_ions_config | n/a | n/a |
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step9_leap_add_ions_output_pdb_path | n/a | n/a |
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step9_leap_add_ions_output_top_path | n/a | n/a |
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step9_leap_add_ions_output_crd_path | n/a | n/a |
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step10_sander_mdrun_energy_config | n/a | n/a |
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step10_sander_mdrun_energy_output_traj_path | n/a | n/a |
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step10_sander_mdrun_energy_output_rst_path | n/a | n/a |
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step10_sander_mdrun_energy_output_log_path | n/a | n/a |
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step11_process_minout_energy_config | n/a | n/a |
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step11_process_minout_energy_output_dat_path | n/a | n/a |
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step12_sander_mdrun_warm_config | n/a | n/a |
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step12_sander_mdrun_warm_output_traj_path | n/a | n/a |
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step12_sander_mdrun_warm_output_rst_path | n/a | n/a |
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step12_sander_mdrun_warm_output_log_path | n/a | n/a |
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step13_process_mdout_warm_config | n/a | n/a |
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step13_process_mdout_warm_output_dat_path | n/a | n/a |
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step14_sander_mdrun_nvt_config | n/a | n/a |
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step14_sander_mdrun_nvt_output_traj_path | n/a | n/a |
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step14_sander_mdrun_nvt_output_rst_path | n/a | n/a |
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step14_sander_mdrun_nvt_output_log_path | n/a | n/a |
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step15_process_mdout_nvt_config | n/a | n/a |
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step15_process_mdout_nvt_output_dat_path | n/a | n/a |
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step16_sander_mdrun_npt_config | n/a | n/a |
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step16_sander_mdrun_npt_output_traj_path | n/a | n/a |
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step16_sander_mdrun_npt_output_rst_path | n/a | n/a |
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step16_sander_mdrun_npt_output_log_path | n/a | n/a |
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step17_process_mdout_npt_config | n/a | n/a |
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step17_process_mdout_npt_output_dat_path | n/a | n/a |
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step18_sander_mdrun_md_config | n/a | n/a |
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step18_sander_mdrun_md_output_traj_path | n/a | n/a |
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step18_sander_mdrun_md_output_rst_path | n/a | n/a |
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step18_sander_mdrun_md_output_log_path | n/a | n/a |
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step19_rmsd_first_config | n/a | n/a |
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step19_rmsd_first_output_cpptraj_path | n/a | n/a |
|
step20_rmsd_exp_config | n/a | n/a |
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step20_rmsd_exp_input_exp_path | n/a | n/a |
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step20_rmsd_exp_output_cpptraj_path | n/a | n/a |
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step21_cpptraj_rgyr_config | n/a | n/a |
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step21_cpptraj_rgyr_output_cpptraj_path | n/a | n/a |
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step22_cpptraj_image_config | n/a | n/a |
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step22_cpptraj_image_output_cpptraj_path | n/a | n/a |
|
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 |
|
step1_pdb4amber_run_out1 | output_pdb_path | Output 3D structure PDB file |
|
step2_leap_gen_top_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step2_leap_gen_top_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step2_leap_gen_top_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step3_sander_mdrun_minH_out1 | output_traj_path | Output trajectory file |
|
step3_sander_mdrun_minH_out2 | output_rst_path | Output restart file |
|
step3_sander_mdrun_minH_out3 | output_log_path | Output log file |
|
step4_process_minout_minH_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step5_sander_mdrun_min_out1 | output_traj_path | Output trajectory file |
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step5_sander_mdrun_min_out2 | output_rst_path | Output restart file |
|
step5_sander_mdrun_min_out3 | output_log_path | Output log file |
|
step6_process_minout_min_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step7_amber_to_pdb_out1 | output_pdb_path | Structure PDB file |
|
step8_leap_solvate_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step8_leap_solvate_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step8_leap_solvate_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step9_leap_add_ions_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step9_leap_add_ions_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step9_leap_add_ions_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step10_sander_mdrun_energy_out1 | output_traj_path | Output trajectory file |
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step10_sander_mdrun_energy_out2 | output_rst_path | Output restart file |
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step10_sander_mdrun_energy_out3 | output_log_path | Output log file |
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step11_process_minout_energy_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
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step12_sander_mdrun_warm_out1 | output_traj_path | Output trajectory file |
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step12_sander_mdrun_warm_out2 | output_rst_path | Output restart file |
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step12_sander_mdrun_warm_out3 | output_log_path | Output log file |
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step13_process_mdout_warm_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step14_sander_mdrun_nvt_out1 | output_traj_path | Output trajectory file |
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step14_sander_mdrun_nvt_out2 | output_rst_path | Output restart file |
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step14_sander_mdrun_nvt_out3 | output_log_path | Output log file |
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step15_process_mdout_nvt_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
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step16_sander_mdrun_npt_out1 | output_traj_path | Output trajectory file |
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step16_sander_mdrun_npt_out2 | output_rst_path | Output restart file |
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step16_sander_mdrun_npt_out3 | output_log_path | Output log file |
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step17_process_mdout_npt_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
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step18_sander_mdrun_md_out1 | output_traj_path | Output trajectory file |
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step18_sander_mdrun_md_out2 | output_rst_path | Output restart file |
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step18_sander_mdrun_md_out3 | output_log_path | Output log file |
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step19_rmsd_first_out1 | output_cpptraj_path | Path to the output processed analysis |
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step20_rmsd_exp_out1 | output_cpptraj_path | Path to the output processed analysis |
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step21_cpptraj_rgyr_out1 | output_cpptraj_path | Path to the output analysis |
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step22_cpptraj_image_out1 | output_cpptraj_path | Path to the output processed trajectory |
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Version History
Version 1 (earliest) Created 10th Jan 2022 at 13:24 by Genís Bayarri
Fetched structure.pdb from URL
Open
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Views: 360 Downloads: 1
Created: 10th Jan 2022 at 13:24
Last updated: 17th Mar 2022 at 10:24
Last used: 28th Jun 2022 at 16:02

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