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.
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Inputs
ID | Name | Description | Type |
---|---|---|---|
step1_leap_gen_top_input_pdb_path | Input file | Input 3D structure PDB file. |
|
step1_leap_gen_top_output_pdb_path | Output file | Output 3D structure PDB file matching the topology file. |
|
step1_leap_gen_top_output_top_path | Output file | Output topology file (AMBER ParmTop). |
|
step1_leap_gen_top_output_crd_path | Output file | Output coordinates file (AMBER crd). |
|
step1_leap_gen_top_config | Config file | Configuration file for biobb_amber.leap_gen_top tool. |
|
step2_leap_solvate_output_pdb_path | Output file | Output 3D structure PDB file matching the topology file. |
|
step2_leap_solvate_output_top_path | Output file | Output topology file (AMBER ParmTop). |
|
step2_leap_solvate_output_crd_path | Output file | Output coordinates file (AMBER crd). |
|
step2_leap_solvate_config | Config file | Configuration file for biobb_amber.leap_solvate tool. |
|
step3_leap_add_ions_output_pdb_path | Output file | Output 3D structure PDB file matching the topology file. |
|
step3_leap_add_ions_output_top_path | Output file | Output topology file (AMBER ParmTop). |
|
step3_leap_add_ions_output_crd_path | Output file | Output coordinates file (AMBER crd). |
|
step3_leap_add_ions_config | Config file | Configuration file for biobb_amber.leap_add_ions tool. |
|
step4_cpptraj_randomize_ions_output_pdb_path | Output file | Structure PDB file with randomized ions. |
|
step4_cpptraj_randomize_ions_output_crd_path | Output file | Structure CRD file with coordinates including randomized ions. |
|
step4_cpptraj_randomize_ions_config | Config file | Configuration file for biobb_amber.cpptraj_randomize_ions tool. |
|
step5_parmed_hmassrepartition_output_top_path | Output file | Output topology file (AMBER ParmTop). |
|
step6_sander_mdrun_eq1_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step6_sander_mdrun_eq1_output_traj_path | Output file | Output trajectory file. |
|
step6_sander_mdrun_eq1_output_rst_path | Output file | Output restart file. |
|
step6_sander_mdrun_eq1_output_log_path | Output file | Output log file. |
|
step6_sander_mdrun_eq1_output_mdinfo_path | Output file | Output MD info. |
|
step6_sander_mdrun_eq1_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step7_process_minout_eq1_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step7_process_minout_eq1_config | Config file | Configuration file for biobb_amber.process_minout tool. |
|
step8_sander_mdrun_eq2_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step8_sander_mdrun_eq2_output_traj_path | Output file | Output trajectory file. |
|
step8_sander_mdrun_eq2_output_rst_path | Output file | Output restart file. |
|
step8_sander_mdrun_eq2_output_log_path | Output file | Output log file. |
|
step8_sander_mdrun_eq2_output_mdinfo_path | Output file | Output MD info. |
|
step8_sander_mdrun_eq2_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step9_process_mdout_eq2_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step9_process_mdout_eq2_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
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step10_sander_mdrun_eq3_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
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step10_sander_mdrun_eq3_output_traj_path | Output file | Output trajectory file. |
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step10_sander_mdrun_eq3_output_rst_path | Output file | Output restart file. |
|
step10_sander_mdrun_eq3_output_log_path | Output file | Output log file. |
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step10_sander_mdrun_eq3_output_mdinfo_path | Output file | Output MD info. |
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step10_sander_mdrun_eq3_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step11_process_minout_eq3_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step11_process_minout_eq3_config | Config file | Configuration file for biobb_amber.process_minout tool. |
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step12_sander_mdrun_eq4_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step12_sander_mdrun_eq4_output_traj_path | Output file | Output trajectory file. |
|
step12_sander_mdrun_eq4_output_rst_path | Output file | Output restart file. |
|
step12_sander_mdrun_eq4_output_log_path | Output file | Output log file. |
|
step12_sander_mdrun_eq4_output_mdinfo_path | Output file | Output MD info. |
|
step12_sander_mdrun_eq4_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step13_process_minout_eq4_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step13_process_minout_eq4_config | Config file | Configuration file for biobb_amber.process_minout tool. |
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step14_sander_mdrun_eq5_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step14_sander_mdrun_eq5_output_traj_path | Output file | Output trajectory file. |
|
step14_sander_mdrun_eq5_output_rst_path | Output file | Output restart file. |
|
step14_sander_mdrun_eq5_output_log_path | Output file | Output log file. |
|
step14_sander_mdrun_eq5_output_mdinfo_path | Output file | Output MD info. |
|
step14_sander_mdrun_eq5_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step15_process_minout_eq5_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step15_process_minout_eq5_config | Config file | Configuration file for biobb_amber.process_minout tool. |
|
step16_sander_mdrun_eq6_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step16_sander_mdrun_eq6_output_traj_path | Output file | Output trajectory file. |
|
step16_sander_mdrun_eq6_output_rst_path | Output file | Output restart file. |
|
step16_sander_mdrun_eq6_output_log_path | Output file | Output log file. |
|
step16_sander_mdrun_eq6_output_mdinfo_path | Output file | Output MD info. |
|
step16_sander_mdrun_eq6_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step17_process_mdout_eq6_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step17_process_mdout_eq6_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
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step18_sander_mdrun_eq7_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step18_sander_mdrun_eq7_output_traj_path | Output file | Output trajectory file. |
|
step18_sander_mdrun_eq7_output_rst_path | Output file | Output restart file. |
|
step18_sander_mdrun_eq7_output_log_path | Output file | Output log file. |
|
step18_sander_mdrun_eq7_output_mdinfo_path | Output file | Output MD info. |
|
step18_sander_mdrun_eq7_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step19_process_mdout_eq7_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step19_process_mdout_eq7_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
|
step20_sander_mdrun_eq8_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step20_sander_mdrun_eq8_output_traj_path | Output file | Output trajectory file. |
|
step20_sander_mdrun_eq8_output_rst_path | Output file | Output restart file. |
|
step20_sander_mdrun_eq8_output_log_path | Output file | Output log file. |
|
step20_sander_mdrun_eq8_output_mdinfo_path | Output file | Output MD info. |
|
step20_sander_mdrun_eq8_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step21_process_mdout_eq8_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step21_process_mdout_eq8_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
|
step22_sander_mdrun_eq9_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step22_sander_mdrun_eq9_output_traj_path | Output file | Output trajectory file. |
|
step22_sander_mdrun_eq9_output_rst_path | Output file | Output restart file. |
|
step22_sander_mdrun_eq9_output_log_path | Output file | Output log file. |
|
step22_sander_mdrun_eq9_output_mdinfo_path | Output file | Output MD info. |
|
step22_sander_mdrun_eq9_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step23_process_mdout_eq9_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step23_process_mdout_eq9_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
|
step24_sander_mdrun_eq10_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step24_sander_mdrun_eq10_output_traj_path | Output file | Output trajectory file. |
|
step24_sander_mdrun_eq10_output_rst_path | Output file | Output restart file. |
|
step24_sander_mdrun_eq10_output_log_path | Output file | Output log file. |
|
step24_sander_mdrun_eq10_output_mdinfo_path | Output file | Output MD info. |
|
step24_sander_mdrun_eq10_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step25_process_mdout_eq10_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
|
step25_process_mdout_eq10_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
|
step26_sander_mdrun_md_input_mdin_path | Input file | Input configuration file (MD run options) (AMBER mdin). |
|
step26_sander_mdrun_md_output_traj_path | Output file | Output trajectory file. |
|
step26_sander_mdrun_md_output_rst_path | Output file | Output restart file. |
|
step26_sander_mdrun_md_output_mdinfo_path | Output file | Output MD info. |
|
step26_sander_mdrun_md_output_log_path | Output file | Output log file. |
|
step26_sander_mdrun_md_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
|
step27_rmsd_first_output_cpptraj_path | Output file | Path to the output processed analysis. |
|
step27_rmsd_first_config | Config file | Configuration file for biobb_analysis.cpptraj_rms tool. |
|
step28_rmsd_exp_output_cpptraj_path | Output file | Path to the output processed analysis. |
|
step28_rmsd_exp_config | Config file | Configuration file for biobb_analysis.cpptraj_rms tool. |
|
step29_cpptraj_rgyr_output_cpptraj_path | Output file | Path to the output analysis. |
|
step29_cpptraj_rgyr_config | Config file | Configuration file for biobb_analysis.cpptraj_rgyr tool. |
|
step30_cpptraj_image_output_cpptraj_path | Output file | Path to the output processed trajectory. |
|
step30_cpptraj_image_config | Config file | Configuration file for biobb_analysis.cpptraj_image tool. |
|
Steps
ID | Name | Description |
---|---|---|
step1_leap_gen_top | leap_gen_top | Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package |
step2_leap_solvate | leap_solvate | Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package |
step3_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 |
step4_cpptraj_randomize_ions | cpptraj_randomize_ions | Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package |
step5_parmed_hmassrepartition | parmed_hmassrepartition | Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package |
step6_sander_mdrun_eq1 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step7_process_minout_eq1 | 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 |
step8_sander_mdrun_eq2 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step9_process_mdout_eq2 | 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 |
step10_sander_mdrun_eq3 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step11_process_minout_eq3 | 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_eq4 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step13_process_minout_eq4 | 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 |
step14_sander_mdrun_eq5 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step15_process_minout_eq5 | 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 |
step16_sander_mdrun_eq6 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step17_process_mdout_eq6 | 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_eq7 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step19_process_mdout_eq7 | 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 |
step20_sander_mdrun_eq8 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step21_process_mdout_eq8 | 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 |
step22_sander_mdrun_eq9 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step23_process_mdout_eq9 | 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 |
step24_sander_mdrun_eq10 | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step25_process_mdout_eq10 | 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 |
step26_sander_mdrun_md | sander_mdrun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step27_rmsd_first | cpptraj_rms | Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory. |
step28_rmsd_exp | cpptraj_rms | Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory. |
step29_cpptraj_rgyr | cpptraj_rgyr | Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory. |
step30_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 |
---|---|---|---|
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. |
|
step27_rmsd_first_out1 | output_cpptraj_path | Path to the output processed analysis. |
|
step28_rmsd_exp_out1 | output_cpptraj_path | Path to the output processed analysis. |
|
step29_cpptraj_rgyr_out1 | output_cpptraj_path | Path to the output analysis. |
|
step30_cpptraj_image_out1 | output_cpptraj_path | Path to the output processed trajectory. |
|
Version History
Version 2 (latest) Created 12th Jun 2023 at 09:27 by Genís Bayarri
Updated workflow descriptors
Frozen
Version-2
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Version 1 (earliest) Created 11th Jan 2022 at 08:14 by Genís Bayarri
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Views: 2610 Downloads: 535
Created: 11th Jan 2022 at 08:14
Last updated: 17th Mar 2022 at 10:44
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