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.
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
ID | Name | Description | Type |
---|---|---|---|
step1_leap_gen_top_config | n/a | n/a |
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step1_leap_gen_top_input_pdb_path | n/a | n/a |
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step1_leap_gen_top_output_pdb_path | n/a | n/a |
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step1_leap_gen_top_output_top_path | n/a | n/a |
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step1_leap_gen_top_output_crd_path | n/a | n/a |
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step2_leap_solvate_config | n/a | n/a |
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step2_leap_solvate_output_pdb_path | n/a | n/a |
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step2_leap_solvate_output_top_path | n/a | n/a |
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step2_leap_solvate_output_crd_path | n/a | n/a |
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step3_leap_add_ions_config | n/a | n/a |
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step3_leap_add_ions_output_pdb_path | n/a | n/a |
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step3_leap_add_ions_output_top_path | n/a | n/a |
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step3_leap_add_ions_output_crd_path | n/a | n/a |
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step4_cpptraj_randomize_ions_config | n/a | n/a |
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step4_cpptraj_randomize_ions_output_pdb_path | n/a | n/a |
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step4_cpptraj_randomize_ions_output_crd_path | n/a | n/a |
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step5_parmed_hmassrepartition_output_top_path | n/a | n/a |
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step6_sander_mdrun_eq1_config | n/a | n/a |
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step6_sander_mdrun_eq1_input_mdin_path | n/a | n/a |
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step6_sander_mdrun_eq1_output_traj_path | n/a | n/a |
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step6_sander_mdrun_eq1_output_rst_path | n/a | n/a |
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step6_sander_mdrun_eq1_output_log_path | n/a | n/a |
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step6_sander_mdrun_eq1_output_mdinfo_path | n/a | n/a |
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step7_process_minout_eq1_config | n/a | n/a |
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step7_process_minout_eq1_output_dat_path | n/a | n/a |
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step8_sander_mdrun_eq2_config | n/a | n/a |
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step8_sander_mdrun_eq2_input_mdin_path | n/a | n/a |
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step8_sander_mdrun_eq2_output_traj_path | n/a | n/a |
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step8_sander_mdrun_eq2_output_rst_path | n/a | n/a |
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step8_sander_mdrun_eq2_output_log_path | n/a | n/a |
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step8_sander_mdrun_eq2_output_mdinfo_path | n/a | n/a |
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step9_process_mdout_eq2_config | n/a | n/a |
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step9_process_mdout_eq2_output_dat_path | n/a | n/a |
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step10_sander_mdrun_eq3_config | n/a | n/a |
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step10_sander_mdrun_eq3_input_mdin_path | n/a | n/a |
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step10_sander_mdrun_eq3_output_traj_path | n/a | n/a |
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step10_sander_mdrun_eq3_output_rst_path | n/a | n/a |
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step10_sander_mdrun_eq3_output_log_path | n/a | n/a |
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step10_sander_mdrun_eq3_output_mdinfo_path | n/a | n/a |
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step11_process_minout_eq3_config | n/a | n/a |
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step11_process_minout_eq3_output_dat_path | n/a | n/a |
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step12_sander_mdrun_eq4_config | n/a | n/a |
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step12_sander_mdrun_eq4_input_mdin_path | n/a | n/a |
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step12_sander_mdrun_eq4_output_traj_path | n/a | n/a |
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step12_sander_mdrun_eq4_output_rst_path | n/a | n/a |
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step12_sander_mdrun_eq4_output_log_path | n/a | n/a |
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step12_sander_mdrun_eq4_output_mdinfo_path | n/a | n/a |
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step13_process_minout_eq4_config | n/a | n/a |
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step13_process_minout_eq4_output_dat_path | n/a | n/a |
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step14_sander_mdrun_eq5_config | n/a | n/a |
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step14_sander_mdrun_eq5_input_mdin_path | n/a | n/a |
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step14_sander_mdrun_eq5_output_traj_path | n/a | n/a |
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step14_sander_mdrun_eq5_output_rst_path | n/a | n/a |
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step14_sander_mdrun_eq5_output_log_path | n/a | n/a |
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step14_sander_mdrun_eq5_output_mdinfo_path | n/a | n/a |
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step15_process_minout_eq5_config | n/a | n/a |
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step15_process_minout_eq5_output_dat_path | n/a | n/a |
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step16_sander_mdrun_eq6_config | n/a | n/a |
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step16_sander_mdrun_eq6_input_mdin_path | n/a | n/a |
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step16_sander_mdrun_eq6_output_traj_path | n/a | n/a |
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step16_sander_mdrun_eq6_output_rst_path | n/a | n/a |
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step16_sander_mdrun_eq6_output_log_path | n/a | n/a |
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step16_sander_mdrun_eq6_output_mdinfo_path | n/a | n/a |
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step17_process_mdout_eq6_config | n/a | n/a |
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step17_process_mdout_eq6_output_dat_path | n/a | n/a |
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step18_sander_mdrun_eq7_config | n/a | n/a |
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step18_sander_mdrun_eq7_input_mdin_path | n/a | n/a |
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step18_sander_mdrun_eq7_output_traj_path | n/a | n/a |
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step18_sander_mdrun_eq7_output_rst_path | n/a | n/a |
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step18_sander_mdrun_eq7_output_log_path | n/a | n/a |
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step18_sander_mdrun_eq7_output_mdinfo_path | n/a | n/a |
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step19_process_mdout_eq7_config | n/a | n/a |
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step19_process_mdout_eq7_output_dat_path | n/a | n/a |
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step20_sander_mdrun_eq8_config | n/a | n/a |
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step20_sander_mdrun_eq8_input_mdin_path | n/a | n/a |
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step20_sander_mdrun_eq8_output_traj_path | n/a | n/a |
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step20_sander_mdrun_eq8_output_rst_path | n/a | n/a |
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step20_sander_mdrun_eq8_output_log_path | n/a | n/a |
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step20_sander_mdrun_eq8_output_mdinfo_path | n/a | n/a |
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step21_process_mdout_eq8_config | n/a | n/a |
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step21_process_mdout_eq8_output_dat_path | n/a | n/a |
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step22_sander_mdrun_eq9_config | n/a | n/a |
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step22_sander_mdrun_eq9_input_mdin_path | n/a | n/a |
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step22_sander_mdrun_eq9_output_traj_path | n/a | n/a |
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step22_sander_mdrun_eq9_output_rst_path | n/a | n/a |
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step22_sander_mdrun_eq9_output_log_path | n/a | n/a |
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step22_sander_mdrun_eq9_output_mdinfo_path | n/a | n/a |
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step23_process_mdout_eq9_config | n/a | n/a |
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step23_process_mdout_eq9_output_dat_path | n/a | n/a |
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step24_sander_mdrun_eq10_config | n/a | n/a |
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step24_sander_mdrun_eq10_input_mdin_path | n/a | n/a |
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step24_sander_mdrun_eq10_output_traj_path | n/a | n/a |
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step24_sander_mdrun_eq10_output_rst_path | n/a | n/a |
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step24_sander_mdrun_eq10_output_log_path | n/a | n/a |
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step24_sander_mdrun_eq10_output_mdinfo_path | n/a | n/a |
|
step25_process_mdout_eq10_config | n/a | n/a |
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step25_process_mdout_eq10_output_dat_path | n/a | n/a |
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step26_sander_mdrun_md_config | n/a | n/a |
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step26_sander_mdrun_md_input_mdin_path | n/a | n/a |
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step26_sander_mdrun_md_output_traj_path | n/a | n/a |
|
step26_sander_mdrun_md_output_rst_path | n/a | n/a |
|
step26_sander_mdrun_md_output_mdinfo_path | n/a | n/a |
|
step26_sander_mdrun_md_output_log_path | n/a | n/a |
|
Steps
ID | Name | Description |
---|---|---|
step1_leap_gen_top | LeapGenTop | Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package |
step2_leap_solvate | LeapSolvate | Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package |
step3_leap_add_ions | LeapAddIons | Adds counterions to a system box for an AMBER MD system using tLeap tool from the AmberTools MD package |
step4_cpptraj_randomize_ions | CpptrajRandomizeIons | Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package |
step5_parmed_hmassrepartition | ParmedHMassRepartition | Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package |
step6_sander_mdrun_eq1 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step7_process_minout_eq1 | 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 |
step8_sander_mdrun_eq2 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step9_process_mdout_eq2 | 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 |
step10_sander_mdrun_eq3 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step11_process_minout_eq3 | 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_eq4 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step13_process_minout_eq4 | 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 |
step14_sander_mdrun_eq5 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step15_process_minout_eq5 | 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 |
step16_sander_mdrun_eq6 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step17_process_mdout_eq6 | 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_eq7 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step19_process_mdout_eq7 | 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 |
step20_sander_mdrun_eq8 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step21_process_mdout_eq8 | 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 |
step22_sander_mdrun_eq9 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step23_process_mdout_eq9 | 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 |
step24_sander_mdrun_eq10 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step25_process_mdout_eq10 | 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 |
step26_sander_mdrun_md | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
Outputs
ID | Name | Description | Type |
---|---|---|---|
step1_leap_gen_top_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step1_leap_gen_top_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step1_leap_gen_top_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step2_leap_solvate_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step2_leap_solvate_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step2_leap_solvate_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step3_leap_add_ions_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step3_leap_add_ions_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step3_leap_add_ions_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step4_cpptraj_randomize_ions_out1 | output_pdb_path | Structure PDB file with randomized ions |
|
step4_cpptraj_randomize_ions_out2 | output_crd_path | Structure CRD file with coordinates including randomized ions |
|
step5_parmed_hmassrepartition_out1 | output_top_path | Output topology file (AMBER ParmTop) |
|
step6_sander_mdrun_eq1_out1 | output_traj_path | Output trajectory file |
|
step6_sander_mdrun_eq1_out2 | output_rst_path | Output restart file |
|
step6_sander_mdrun_eq1_out3 | output_log_path | Output log file |
|
step6_sander_mdrun_eq1_out4 | output_mdinfo_path | Output MD info |
|
step7_process_minout_eq1_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step8_sander_mdrun_eq2_out1 | output_traj_path | Output trajectory file |
|
step8_sander_mdrun_eq2_out2 | output_rst_path | Output restart file |
|
step8_sander_mdrun_eq2_out3 | output_log_path | Output log file |
|
step8_sander_mdrun_eq2_out4 | output_mdinfo_path | Output MD info |
|
step9_process_mdout_eq2_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step10_sander_mdrun_eq3_out1 | output_traj_path | Output trajectory file |
|
step10_sander_mdrun_eq3_out2 | output_rst_path | Output restart file |
|
step10_sander_mdrun_eq3_out3 | output_log_path | Output log file |
|
step10_sander_mdrun_eq3_out4 | output_mdinfo_path | Output MD info |
|
step11_process_minout_eq3_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step12_sander_mdrun_eq4_out1 | output_traj_path | Output trajectory file |
|
step12_sander_mdrun_eq4_out2 | output_rst_path | Output restart file |
|
step12_sander_mdrun_eq4_out3 | output_log_path | Output log file |
|
step12_sander_mdrun_eq4_out4 | output_mdinfo_path | Output MD info |
|
step13_process_minout_eq4_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step14_sander_mdrun_eq5_out1 | output_traj_path | Output trajectory file |
|
step14_sander_mdrun_eq5_out2 | output_rst_path | Output restart file |
|
step14_sander_mdrun_eq5_out3 | output_log_path | Output log file |
|
step14_sander_mdrun_eq5_out4 | output_mdinfo_path | Output MD info |
|
step15_process_minout_eq5_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step16_sander_mdrun_eq6_out1 | output_traj_path | Output trajectory file |
|
step16_sander_mdrun_eq6_out2 | output_rst_path | Output restart file |
|
step16_sander_mdrun_eq6_out3 | output_log_path | Output log file |
|
step16_sander_mdrun_eq6_out4 | output_mdinfo_path | Output MD info |
|
step17_process_mdout_eq6_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step18_sander_mdrun_eq7_out1 | output_traj_path | Output trajectory file |
|
step18_sander_mdrun_eq7_out2 | output_rst_path | Output restart file |
|
step18_sander_mdrun_eq7_out3 | output_log_path | Output log file |
|
step18_sander_mdrun_eq7_out4 | output_mdinfo_path | Output MD info |
|
step19_process_mdout_eq7_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step20_sander_mdrun_eq8_out1 | output_traj_path | Output trajectory file |
|
step20_sander_mdrun_eq8_out2 | output_rst_path | Output restart file |
|
step20_sander_mdrun_eq8_out3 | output_log_path | Output log file |
|
step20_sander_mdrun_eq8_out4 | output_mdinfo_path | Output MD info |
|
step21_process_mdout_eq8_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step22_sander_mdrun_eq9_out1 | output_traj_path | Output trajectory file |
|
step22_sander_mdrun_eq9_out2 | output_rst_path | Output restart file |
|
step22_sander_mdrun_eq9_out3 | output_log_path | Output log file |
|
step22_sander_mdrun_eq9_out4 | output_mdinfo_path | Output MD info |
|
step23_process_mdout_eq9_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step24_sander_mdrun_eq10_out1 | output_traj_path | Output trajectory file |
|
step24_sander_mdrun_eq10_out2 | output_rst_path | Output restart file |
|
step24_sander_mdrun_eq10_out3 | output_log_path | Output log file |
|
step24_sander_mdrun_eq10_out4 | output_mdinfo_path | Output MD info |
|
step25_process_mdout_eq10_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step26_sander_mdrun_md_out1 | output_traj_path | Output trajectory file |
|
step26_sander_mdrun_md_out2 | output_rst_path | Output restart file |
|
step26_sander_mdrun_md_out3 | output_mdinfo_path | Output MD info |
|
step26_sander_mdrun_md_out4 | output_log_path | Output log file |
|
Version History
Version 2 (latest) Created 12th Jun 2023 at 09:27 by Genís Bayarri
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Version 1 (earliest) Created 11th Jan 2022 at 08:14 by Genís Bayarri
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Created: 11th Jan 2022 at 08:14
Last updated: 17th Mar 2022 at 10:44
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