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 |
---|---|---|---|
step000_reduce_remove_hydrogens_input_path | Input file | Path to the input file. |
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step000_reduce_remove_hydrogens_output_path | Output file | Path to the output file. |
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step00_extract_molecule_output_molecule_path | Output file | Output molecule file path. |
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step0000_cat_pdb_input_structure2 | Input file | Input structure 2 file path. |
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step0000_cat_pdb_output_structure_path | Output file | Output protein file path. |
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step0_cat_pdb_input_structure2 | Input file | Input structure 2 file path. |
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step0_cat_pdb_output_structure_path | Output file | Output protein file path. |
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step1_pdb4amber_run_output_pdb_path | Output file | Output 3D structure PDB file. |
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step2_leap_gen_top_input_lib_path | Input file | Input ligand library parameters file. |
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step2_leap_gen_top_input_frcmod_path | Input file | Input ligand frcmod parameters file. |
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step2_leap_gen_top_output_pdb_path | Output file | Output 3D structure PDB file matching the topology file. |
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step2_leap_gen_top_output_top_path | Output file | Output topology file (AMBER ParmTop). |
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step2_leap_gen_top_output_crd_path | Output file | Output coordinates file (AMBER crd). |
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step2_leap_gen_top_config | Config file | Configuration file for biobb_amber.leap_gen_top tool. |
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step3_sander_mdrun_minH_output_traj_path | Output file | Output trajectory file. |
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step3_sander_mdrun_minH_output_rst_path | Output file | Output restart file. |
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step3_sander_mdrun_minH_output_log_path | Output file | Output log file. |
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step3_sander_mdrun_minH_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step4_process_minout_minH_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
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step4_process_minout_minH_config | Config file | Configuration file for biobb_amber.process_minout tool. |
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step5_sander_mdrun_min_output_traj_path | Output file | Output trajectory file. |
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step5_sander_mdrun_min_output_rst_path | Output file | Output restart file. |
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step5_sander_mdrun_min_output_log_path | Output file | Output log file. |
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step5_sander_mdrun_min_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step6_process_minout_min_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
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step6_process_minout_min_config | Config file | Configuration file for biobb_amber.process_minout tool. |
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step7_amber_to_pdb_output_pdb_path | Output file | Structure PDB file. |
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step8_leap_solvate_input_lib_path | Input file | Input ligand library parameters file. |
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step8_leap_solvate_input_frcmod_path | Input file | Input ligand frcmod parameters file. |
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step8_leap_solvate_output_pdb_path | Output file | Output 3D structure PDB file matching the topology file. |
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step8_leap_solvate_output_top_path | Output file | Output topology file (AMBER ParmTop). |
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step8_leap_solvate_output_crd_path | Output file | Output coordinates file (AMBER crd). |
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step8_leap_solvate_config | Config file | Configuration file for biobb_amber.leap_solvate tool. |
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step9_leap_add_ions_input_lib_path | Input file | Input ligand library parameters file. |
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step9_leap_add_ions_input_frcmod_path | Input file | Input ligand frcmod parameters file. |
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step9_leap_add_ions_output_pdb_path | Output file | Output 3D structure PDB file matching the topology file. |
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step9_leap_add_ions_output_top_path | Output file | Output topology file (AMBER ParmTop). |
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step9_leap_add_ions_output_crd_path | Output file | Output coordinates file (AMBER crd). |
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step9_leap_add_ions_config | Config file | Configuration file for biobb_amber.leap_add_ions tool. |
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step10_sander_mdrun_energy_output_traj_path | Output file | Output trajectory file. |
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step10_sander_mdrun_energy_output_rst_path | Output file | Output restart file. |
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step10_sander_mdrun_energy_output_log_path | Output file | Output log file. |
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step10_sander_mdrun_energy_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step11_process_minout_energy_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
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step11_process_minout_energy_config | Config file | Configuration file for biobb_amber.process_minout tool. |
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step12_sander_mdrun_warm_output_traj_path | Output file | Output trajectory file. |
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step12_sander_mdrun_warm_output_rst_path | Output file | Output restart file. |
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step12_sander_mdrun_warm_output_log_path | Output file | Output log file. |
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step12_sander_mdrun_warm_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step13_process_mdout_warm_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
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step13_process_mdout_warm_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
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step14_sander_mdrun_nvt_output_traj_path | Output file | Output trajectory file. |
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step14_sander_mdrun_nvt_output_rst_path | Output file | Output restart file. |
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step14_sander_mdrun_nvt_output_log_path | Output file | Output log file. |
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step14_sander_mdrun_nvt_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step15_process_mdout_nvt_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
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step15_process_mdout_nvt_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
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step16_sander_mdrun_npt_output_traj_path | Output file | Output trajectory file. |
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step16_sander_mdrun_npt_output_rst_path | Output file | Output restart file. |
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step16_sander_mdrun_npt_output_log_path | Output file | Output log file. |
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step16_sander_mdrun_npt_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step17_process_mdout_npt_output_dat_path | Output file | Dat output file containing data from the specified terms along the minimization process. |
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step17_process_mdout_npt_config | Config file | Configuration file for biobb_amber.process_mdout tool. |
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step18_sander_mdrun_md_output_traj_path | Output file | Output trajectory file. |
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step18_sander_mdrun_md_output_rst_path | Output file | Output restart file. |
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step18_sander_mdrun_md_output_log_path | Output file | Output log file. |
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step18_sander_mdrun_md_config | Config file | Configuration file for biobb_amber.sander_mdrun tool. |
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step19_rmsd_first_output_cpptraj_path | Output file | Path to the output processed analysis. |
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step19_rmsd_first_config | Config file | Configuration file for biobb_analysis.cpptraj_rms tool. |
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step20_rmsd_exp_output_cpptraj_path | Output file | Path to the output processed analysis. |
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step20_rmsd_exp_config | Config file | Configuration file for biobb_analysis.cpptraj_rms tool. |
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step21_cpptraj_rgyr_output_cpptraj_path | Output file | Path to the output analysis. |
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step21_cpptraj_rgyr_config | Config file | Configuration file for biobb_analysis.cpptraj_rgyr tool. |
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step22_cpptraj_image_output_cpptraj_path | Output file | Path to the output processed trajectory. |
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step22_cpptraj_image_config | Config file | Configuration file for biobb_analysis.cpptraj_image tool. |
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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. |
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step00_extract_molecule_out1 | output_molecule_path | Output molecule file path. |
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step0000_cat_pdb_out1 | output_structure_path | Output protein file path. |
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step0_cat_pdb_out1 | output_structure_path | Output protein file path. |
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step1_pdb4amber_run_out1 | output_pdb_path | Output 3D structure PDB file. |
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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. |
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step3_sander_mdrun_minH_out2 | output_rst_path | Output restart file. |
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step3_sander_mdrun_minH_out3 | output_log_path | Output log file. |
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step4_process_minout_minH_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process. |
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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. |
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step5_sander_mdrun_min_out3 | output_log_path | Output log file. |
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step6_process_minout_min_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process. |
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step7_amber_to_pdb_out1 | output_pdb_path | Structure PDB file. |
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step8_leap_solvate_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file. |
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step8_leap_solvate_out2 | output_top_path | Output topology file (AMBER ParmTop). |
|
step8_leap_solvate_out3 | output_crd_path | Output coordinates file (AMBER crd). |
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step9_leap_add_ions_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file. |
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step9_leap_add_ions_out2 | output_top_path | Output topology file (AMBER ParmTop). |
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step9_leap_add_ions_out3 | output_crd_path | Output coordinates file (AMBER crd). |
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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. |
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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. |
|
step22_cpptraj_image_out1 | output_cpptraj_path | Path to the output processed trajectory. |
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Version History
Version 2 (latest) Created 9th Jun 2023 at 07:44 by Genís Bayarri
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Version 1 (earliest) Created 10th Jan 2022 at 15:27 by Genís Bayarri
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Created: 10th Jan 2022 at 15:27
Last updated: 17th Mar 2022 at 10:35
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